Network approaches and applications in biology

Trey Ideker, Ruth Nussinov

PLOS Computational Biology: published October 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005771

Ten simple rules for writing a response to reviewers

William Stafford Noble

PLOS Computational Biology: published October 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005730

Ten simple rules in considering a career in academia versus government

Philip E. Bourne

PLOS Computational Biology: published October 5, 2017 | https://doi.org/10.1371/journal.pcbi.1005729

Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators

Lindsay Barone, Jason Williams, David Micklos

PLOS Computational Biology: published October 19, 2017 | https://doi.org/10.1371/journal.pcbi.1005755

Related Articles

1. Correction: Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators

Learning infectious disease epidemiology in a modern framework

Andreas Handel

PLOS Computational Biology: published October 19, 2017 | https://doi.org/10.1371/journal.pcbi.1005642

Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience

Kim T. Gurwitz, Shaun Aron, Sumir Panji, Suresh Maslamoney, Pedro L. Fernandes, David P. Judge, Amel Ghouila, Jean-Baka Domelevo Entfellner, Fatma Z. Guerfali, Colleen Saunders, Ahmed Mansour Alzohairy, Samson P. Salifu, Rehab Ahmed, Ruben Cloete, Jonathan Kayondo, Deogratius Ssemwanga, Nicola Mulder, H3ABioNet Consortium's Education Training and Working Group as members of the H3Africa Consortium

PLOS Computational Biology: published October 5, 2017 | https://doi.org/10.1371/journal.pcbi.1005715

Structural host-microbiota interaction networks

Emine Guven-Maiorov, Chung-Jung Tsai, Ruth Nussinov

PLOS Computational Biology: published October 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005579

Maximum entropy methods for extracting the learned features of deep neural networks

Alex Finnegan, Jun S. Song

PLOS Computational Biology: published October 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005836

Concerted regulation of npc2 binding to endosomal/lysosomal membranes by bis(monoacylglycero)phosphate and sphingomyelin

Giray Enkavi, Heikki Mikkolainen, Burçin Güngör, Elina Ikonen, Ilpo Vattulainen

PLOS Computational Biology: published October 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005831

A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling

Vijay Vedula, Juhyun Lee, Hao Xu, C.-C. Jay Kuo, Tzung K. Hsiai, Alison L. Marsden

PLOS Computational Biology: published October 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005828

Related Articles

1. Correction: A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling

A mechanistic spatio-temporal framework for modelling individual-to-individual transmission—With an application to the 2014-2015 West Africa Ebola outbreak

Max S. Y. Lau, Gavin J. Gibson, Hola Adrakey, Amanda McClelland, Steven Riley, Jon Zelner, George Streftaris, Sebastian Funk, Jessica Metcalf, Benjamin D. Dalziel, Bryan T. Grenfell

PLOS Computational Biology: published October 30, 2017 | https://doi.org/10.1371/journal.pcbi.1005798

The influence of astrocytes on the width of orientation hypercolumns in visual cortex: A computational perspective

Ryan T. Philips, Mriganka Sur, V. Srinivasa Chakravarthy

PLOS Computational Biology: published October 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005785

Point process analysis of noise in early invertebrate vision

Kris V. Parag, Glenn Vinnicombe

PLOS Computational Biology: published October 27, 2017 | https://doi.org/10.1371/journal.pcbi.1005687

Unified thalamic model generates multiple distinct oscillations with state-dependent entrainment by stimulation

Guoshi Li, Craig S. Henriquez, Flavio Fröhlich

PLOS Computational Biology: published October 26, 2017 | https://doi.org/10.1371/journal.pcbi.1005797

Modeling the adenosine system as a modulator of cognitive performance and sleep patterns during sleep restriction and recovery

Andrew J. K. Phillips, Elizabeth B. Klerman, James P. Butler

PLOS Computational Biology: published October 26, 2017 | https://doi.org/10.1371/journal.pcbi.1005759

Dynamics and heterogeneity of brain damage in multiple sclerosis

Ekaterina Kotelnikova, Narsis A. Kiani, Elena Abad, Elena H. Martinez-Lapiscina, Magi Andorra, Irati Zubizarreta, Irene Pulido-Valdeolivas, Inna Pertsovskaya, Leonidas G. Alexopoulos, Tomas Olsson, Roland Martin, Friedemann Paul, Jesper Tegnér, Jordi Garcia-Ojalvo, Pablo Villoslada

PLOS Computational Biology: published October 26, 2017 | https://doi.org/10.1371/journal.pcbi.1005757

Transcriptomic correlates of neuron electrophysiological diversity

Shreejoy J. Tripathy, Lilah Toker, Brenna Li, Cindy-Lee Crichlow, Dmitry Tebaykin, B. Ogan Mancarci, Paul Pavlidis

PLOS Computational Biology: published October 25, 2017 | https://doi.org/10.1371/journal.pcbi.1005814

Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics

Nicolas E Martin, Siddharth Malik, Nicolas Calimet, Jean-Pierre Changeux, Marco Cecchini

PLOS Computational Biology: published October 25, 2017 | https://doi.org/10.1371/journal.pcbi.1005784

Neural field model to reconcile structure with function in primary visual cortex

James Rankin, Frédéric Chavane

PLOS Computational Biology: published October 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005821

Scaffolding the cup-shaped double membrane in autophagy

Amir Houshang Bahrami, Mary G. Lin, Xuefeng Ren, James H. Hurley, Gerhard Hummer

PLOS Computational Biology: published October 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005817

Identification of immune signatures predictive of clinical protection from malaria

John Joseph Valletta, Mario Recker

PLOS Computational Biology: published October 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005812

Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time

Anna Hake, Nico Pfeifer

PLOS Computational Biology: published October 24, 2017 | https://doi.org/10.1371/journal.pcbi.1005789

Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network

Cynthia Sandor, Nicola L. Beer, Caleb Webber

PLOS Computational Biology: published October 23, 2017 | https://doi.org/10.1371/journal.pcbi.1005816

Automated deconvolution of structured mixtures from heterogeneous tumor genomic data

Theodore Roman, Lu Xie, Russell Schwartz

PLOS Computational Biology: published October 23, 2017 | https://doi.org/10.1371/journal.pcbi.1005815

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization

Claire N. Bedbrook, Kevin K. Yang, Austin J. Rice, Viviana Gradinaru, Frances H. Arnold

PLOS Computational Biology: published October 23, 2017 | https://doi.org/10.1371/journal.pcbi.1005786

Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition

Timothy N. Rubin, Oluwasanmi Koyejo, Krzysztof J. Gorgolewski, Michael N. Jones, Russell A. Poldrack, Tal Yarkoni

PLOS Computational Biology: published October 23, 2017 | https://doi.org/10.1371/journal.pcbi.1005649

Distinct prediction errors in mesostriatal circuits of the human brain mediate learning about the values of both states and actions: evidence from high-resolution fMRI

Jaron T. Colas, Wolfgang M. Pauli, Tobias Larsen, J. Michael Tyszka, John P. O’Doherty

PLOS Computational Biology: published October 19, 2017 | https://doi.org/10.1371/journal.pcbi.1005810

Quantifying the strength of quorum sensing crosstalk within microbial communities

Kalinga Pavan T. Silva, Prithiviraj Chellamuthu, James Q. Boedicker

PLOS Computational Biology: published October 19, 2017 | https://doi.org/10.1371/journal.pcbi.1005809

Deconvolving sequence features that discriminate between overlapping regulatory annotations

Akshay Kakumanu, Silvia Velasco, Esteban Mazzoni, Shaun Mahony

PLOS Computational Biology: published October 19, 2017 | https://doi.org/10.1371/journal.pcbi.1005795

Seasonality in risk of pandemic influenza emergence

Spencer J. Fox, Joel C. Miller, Lauren Ancel Meyers

PLOS Computational Biology: published October 19, 2017 | https://doi.org/10.1371/journal.pcbi.1005749

A deep convolutional neural network for classification of red blood cells in sickle cell anemia

Mengjia Xu, Dimitrios P. Papageorgiou, Sabia Z. Abidi, Ming Dao, Hong Zhao, George Em Karniadakis

PLOS Computational Biology: published October 19, 2017 | https://doi.org/10.1371/journal.pcbi.1005746

Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics

Roman Shevchuk, Jochen S. Hub

PLOS Computational Biology: published October 18, 2017 | https://doi.org/10.1371/journal.pcbi.1005800

Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster

Cen Wan, Jonathan G. Lees, Federico Minneci, Christine A. Orengo, David T. Jones

PLOS Computational Biology: published October 18, 2017 | https://doi.org/10.1371/journal.pcbi.1005791

A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data

Nan Lin, Yun Zhu, Ruzong Fan, Momiao Xiong

PLOS Computational Biology: published October 17, 2017 | https://doi.org/10.1371/journal.pcbi.1005788

A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action

Shiran Abadi, Winston X. Yan, David Amar, Itay Mayrose

PLOS Computational Biology: published October 16, 2017 | https://doi.org/10.1371/journal.pcbi.1005807

Clusternomics: Integrative context-dependent clustering for heterogeneous datasets

Evelina Gabasova, John Reid, Lorenz Wernisch

PLOS Computational Biology: published October 16, 2017 | https://doi.org/10.1371/journal.pcbi.1005781

The role of glutamate in neuronal ion homeostasis: A case study of spreading depolarization

Niklas Hübel, Mahshid S. Hosseini-Zare, Jokūbas Žiburkus, Ghanim Ullah

PLOS Computational Biology: published October 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005804

BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions

Phuong Dao, Yoo-Ah Kim, Damian Wojtowicz, Sanna Madan, Roded Sharan, Teresa M. Przytycka

PLOS Computational Biology: published October 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005695

Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets

Kevin Drew, Christian L. Müller, Richard Bonneau, Edward M. Marcotte

PLOS Computational Biology: published October 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005625

Vicus: Exploiting local structures to improve network-based analysis of biological data

Bo Wang, Lin Huang, Yuke Zhu, Anshul Kundaje, Serafim Batzoglou, Anna Goldenberg

PLOS Computational Biology: published October 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005621

Systematic, network-based characterization of therapeutic target inhibitors

Yao Shen, Mariano J. Alvarez, Brygida Bisikirska, Alexander Lachmann, Ronald Realubit, Sergey Pampou, Jorida Coku, Charles Karan, Andrea Califano

PLOS Computational Biology: published October 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005599

Network propagation in the cytoscape cyberinfrastructure

Daniel E. Carlin, Barry Demchak, Dexter Pratt, Eric Sage, Trey Ideker

PLOS Computational Biology: published October 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005598

Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases

Aziz M. Mezlini, Anna Goldenberg

PLOS Computational Biology: published October 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005580

Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology

Kevin S. Bonham, Melanie I. Stefan

PLOS Computational Biology: published October 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005134

The structured ‘low temperature’ phase of the retinal population code

Mark L. Ioffe, Michael J. Berry II

PLOS Computational Biology: published October 11, 2017 | https://doi.org/10.1371/journal.pcbi.1005792

General principles of binding between cell surface receptors and multi-specific ligands: A computational study

Jiawen Chen, Steven C. Almo, Yinghao Wu

PLOS Computational Biology: published October 10, 2017 | https://doi.org/10.1371/journal.pcbi.1005805

Neural coding in the visual system of Drosophila melanogaster: How do small neural populations support visually guided behaviours?

Alex D. M. Dewar, Antoine Wystrach, Andrew Philippides, Paul Graham

PLOS Computational Biology: published October 10, 2017 | https://doi.org/10.1371/journal.pcbi.1005735

Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments

Peter Ashcroft, Markus G. Manz, Sebastian Bonhoeffer

PLOS Computational Biology: published October 9, 2017 | https://doi.org/10.1371/journal.pcbi.1005803

Image-based model of the spectrin cytoskeleton for red blood cell simulation

Thomas G. Fai, Alejandra Leo-Macias, David L. Stokes, Charles S. Peskin

PLOS Computational Biology: published October 9, 2017 | https://doi.org/10.1371/journal.pcbi.1005790

Object detection through search with a foveated visual system

Emre Akbas, Miguel P. Eckstein

PLOS Computational Biology: published October 9, 2017 | https://doi.org/10.1371/journal.pcbi.1005743

A Bayesian approach to modelling heterogeneous calcium responses in cell populations

Agne Tilūnaitė, Wayne Croft, Noah Russell, Tomas C. Bellamy, Rüdiger Thul

PLOS Computational Biology: published October 6, 2017 | https://doi.org/10.1371/journal.pcbi.1005794

The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths

Gudrun Gygli, Maria Fátima Lucas, Victor Guallar, Willem J. H. van Berkel

PLOS Computational Biology: published October 6, 2017 | https://doi.org/10.1371/journal.pcbi.1005787

Inferring oscillatory modulation in neural spike trains

Kensuke Arai, Robert E. Kass

PLOS Computational Biology: published October 6, 2017 | https://doi.org/10.1371/journal.pcbi.1005596

A unifying Bayesian account of contextual effects in value-based choice

Francesco Rigoli, Christoph Mathys, Karl J. Friston, Raymond J. Dolan

PLOS Computational Biology: published October 5, 2017 | https://doi.org/10.1371/journal.pcbi.1005769

Related Articles

1. Correction: A unifying Bayesian account of contextual effects in value-based choice

Differential temperature sensitivity of synaptic and firing processes in a neural mass model of epileptic discharges explains heterogeneous response of experimental epilepsy to focal brain cooling

Jaymar Soriano, Takatomi Kubo, Takao Inoue, Hiroyuki Kida, Toshitaka Yamakawa, Michiyasu Suzuki, Kazushi Ikeda

PLOS Computational Biology: published October 5, 2017 | https://doi.org/10.1371/journal.pcbi.1005736

The evolutionary origins of Lévy walk foraging

Marina E. Wosniack, Marcos C. Santos, Ernesto P. Raposo, Gandhi M. Viswanathan, Marcos G. E. da Luz

PLOS Computational Biology: published October 3, 2017 | https://doi.org/10.1371/journal.pcbi.1005774

Identifying parameter regions for multistationarity

Carsten Conradi, Elisenda Feliu, Maya Mincheva, Carsten Wiuf

PLOS Computational Biology: published October 3, 2017 | https://doi.org/10.1371/journal.pcbi.1005751

Signatures of criticality arise from random subsampling in simple population models

Marcel Nonnenmacher, Christian Behrens, Philipp Berens, Matthias Bethge, Jakob H. Macke

PLOS Computational Biology: published October 3, 2017 | https://doi.org/10.1371/journal.pcbi.1005718

Related Articles

1. Correction: Signatures of criticality arise from random subsampling in simple population models

A single-cell spiking model for the origin of grid-cell patterns

Tiziano D’Albis, Richard Kempter

PLOS Computational Biology: published October 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005782

A theoretical framework for analyzing coupled neuronal networks: Application to the olfactory system

Andrea K. Barreiro, Shree Hari Gautam, Woodrow L. Shew, Cheng Ly

PLOS Computational Biology: published October 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005780

Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing

Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford

PLOS Computational Biology: published October 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005777

Estimating time of HIV-1 infection from next-generation sequence diversity

Vadim Puller, Richard Neher, Jan Albert

PLOS Computational Biology: published October 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005775

A continuum-mechanical skeletal muscle model including actin-titin interaction predicts stable contractions on the descending limb of the force-length relation

Thomas Heidlauf, Thomas Klotz, Christian Rode, Tobias Siebert, Oliver Röhrle

PLOS Computational Biology: published October 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005773

Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models

Vahid Rostami, PierGianLuca Porta Mana, Sonja Grün, Moritz Helias

PLOS Computational Biology: published October 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005762

Learning causal networks with latent variables from multivariate information in genomic data

Louis Verny, Nadir Sella, Séverine Affeldt, Param Priya Singh, Hervé Isambert

PLOS Computational Biology: published October 2, 2017 | https://doi.org/10.1371/journal.pcbi.1005662