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PLOS Computational Biology

ISSN Print: 1553-734X

ISSN Online:

Website: http://www.ploscompbiol.org/article/browse/volume

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Ten Simple Rules for a Bioinformatics Journal Club

Andrew Lonsdale？,Jocelyn Sietsma Penington？,Timothy Rice？,Michael Walker？,Harriet Dashnow

Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling

Roland Keller？,Marcus Klein？,Maria Thomas？,Andreas Dr？ger？,Ute Metzger？,Markus F. Templin？,Thomas O. Joos？,Wolfgang E. Thasler？,Andreas Zell？,Ulrich M. Zanger

Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family

Almudena Pino-Angeles？,John M. Leveritt III？,Themis Lazaridis

Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities

Maria E. Tomasso？,Micheal J. Tarver？,Deepa Devarajan？,Steven T. Whitten

Coenzyme Q Biosynthesis: Evidence for a Substrate Access Channel in the FAD-Dependent Monooxygenase Coq6

Alexandre Is？,Vincent Leroux？,Myriam Smadja？,Lucie Gonzalez？,Murielle Lombard？,Fabien Pierrel？,Caroline Mellot-Draznieks？,Marc Fontecave

A Quick Introduction to Version Control with Git and GitHub

John D. Blischak？,Emily R. Davenport？,Greg Wilson

Computational Modeling, Formal Analysis, and Tools for Systems Biology

Ezio Bartocci？,Pietro Lió

Does High-Dose Antimicrobial Chemotherapy Prevent the Evolution of Resistance?

Troy Day？,Andrew F. Read

Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach

Isaure Chauvot de Beauchene？,Sjoerd J. de Vries？,Martin Zacharias

Optimal Population-Level Infection Detection Strategies for Malaria Control and Elimination in a Spatial Model of Malaria Transmission

Jaline Gerardin？,Caitlin A. Bever？,Busiku Hamainza？,John M. Miller？,Philip A. Eckhoff？,Edward A. Wenger

Evidence for Functional Groupings of Vibrissae across the Rodent Mystacial Pad

Jennifer A. Hobbs？,R. Blythe Towal？,Mitra J. Z. Hartmann

Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates

Marco A. Deriu？,Gianvito Grasso？,Jack A. Tuszynski？,Diego Gallo？,Umberto Morbiducci？,Andrea Danani

Model-Based Analysis of Cell Cycle Responses to Dynamically Changing Environments

Daniel D Seaton？,J Krishnan

Residual Viremia in Treated HIV+ Individuals

Jessica M. Conway？,Alan S. Perelson

Neurally Encoding Time for Olfactory Navigation

In Jun Park？,Andrew M. Hein？,Yuriy V. Bobkov？,Matthew A. Reidenbach？,Barry W. Ache？,Jose C. Principe

Discovery of Influenza A Virus Sequence Pairs and Their Combinations for Simultaneous Heterosubtypic Targeting that Hedge against Antiviral Resistance

Keng Boon Wee？,Raphael Tze Chuen Lee？,Jing Lin？,Zacharias Aloysius Dwi Pramono？,Sebastian Maurer-Stroh

Brain Connectivity Dissociates Responsiveness from Drug Exposure during Propofol-Induced Transitions of Consciousness

Srivas Chennu？,Stuart O’Connor？,Ram Adapa？,David K. Menon？,Tristan A. Bekinschtein

Long-Lasting Sparks: Multi-Metastability and Release Competition in the Calcium Release Unit Network

Zhen Song？,Alain Karma？,James N. Weiss？,Zhilin Qu

Transient Accumulation of NO2- and N2O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes

Junaid Hassan？,Zhi Qu？,Linda L. Bergaust？,Lars R. Bakken

Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines

Andrea N. Kravats？,Sam Tonddast-Navaei？,George Stan

Faster Adaptation in Smaller Populations: Counterintuitive Evolution of HIV during Childhood Infection

Jayna Raghwani？,Samir Bhatt？,Oliver G. Pybus

Spontaneous Decoding of the Timing and Content of Human Object Perception from Cortical Surface Recordings Reveals Complementary Information in the Event-Related Potential and Broadband Spectral Change

Kai J. Miller？,Gerwin Schalk？,Dora Hermes？,Jeffrey G. Ojemann？,Rajesh P. N. Rao

A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation

Iman Farasat？,Howard M. Salis

Modelling Feedback Excitation, Pacemaker Properties and Sensory Switching of Electrically Coupled Brainstem Neurons Controlling Rhythmic Activity

Michael J. Hull？,Stephen R. Soffe？,David J. Willshaw？,Alan Roberts

K+ Block Is the Mechanism of Functional Asymmetry in Bacterial Nav Channels

Van Ngo？,Yibo Wang？,Stephan Haas？,Sergei Y. Noskov？,Robert A. Farley

Probing the Limits to MicroRNA-Mediated Control of Gene Expression

Araks Martirosyan？,Matteo Figliuzzi？,Enzo Marinari？,Andrea De Martino

A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae

Susanne Gerber？,Martina Fr？hlich？,Hella Lichtenberg-Fraté？,Sergey Shabala？,Lana Shabala？,Edda Klipp

Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles

Olga Kononova？,Joost Snijder？,Yaroslav Kholodov？,Kenneth A. Marx？,Gijs J. L. Wuite？,Wouter H. Roos？,Valeri Barsegov

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli

Matthew A. Oberhardt？,Raphy Zarecki？,Leah Reshef？,Fangfang Xia？,Miquel Duran-Frigola？,Rachel Schreiber？,Christopher S. Henry？,Nir Ben-Tal？,Daniel J. Dwyer？,Uri Gophna

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics

David Lamparter？,Daniel Marbach？,Rico Rueedi？,Zoltán Kutalik？,Sven Bergmann

Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance

C. Brandon Ogbunugafor？,C. Scott Wylie？,Ibrahim Diakite？,Daniel M. Weinreich？,Daniel L. Hartl

Social Norms of Cooperation in Small-Scale Societies

Fernando P. Santos？,Francisco C. Santos？,Jorge M. Pacheco

A Computational Model for the AMPA Receptor Phosphorylation Master Switch Regulating Cerebellar Long-Term Depression

Andrew R. Gallimore？,A. Radu Aricescu？,Michisuke Yuzaki？,Radu Calinescu

Evolutionary and Functional Relationships in the Truncated Hemoglobin Family

Juan P. Bustamante？,Leandro Radusky？,Leonardo Boechi？,Darío A. Estrin？,Arjen ten Have？,Marcelo A. Martí

Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation

Duncan K. Ralph？,Frederick A. Matsen IV

Spatial Metrics of Tumour Vascular Organisation Predict Radiation Efficacy in a Computational Model

Jacob G. Scott？,Alexander G. Fletcher？,Alexander R. A. Anderson？,Philip K. Maini

Measuring Integrated Information from the Decoding Perspective

Masafumi Oizumi？,Shun-ichi Amari？,Toru Yanagawa？,Naotaka Fujii？,Naotsugu Tsuchiya

Model-Based Comprehensive Analysis of School Closure Policies for Mitigating Influenza Epidemics and Pandemics

Laura Fumanelli？,Marco Ajelli？,Stefano Merler？,Neil M. Ferguson？,Simon Cauchemez

Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation

Lin Chao？,Camilla Ulla Rang？,Audrey Menegaz Proenca？,Jasper Ubirajara Chao

A Network Model to Describe the Terminal Differentiation of B Cells

Akram Méndez？,Luis Mendoza

The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel

Samira Yazdi？,Matthias Stein？,Fredrik Elinder？,Magnus Andersson？,Erik Lindahl

Recovery of Dynamics and Function in Spiking Neural Networks with Closed-Loop Control

Ioannis Vlachos？,Ta？kin Deniz？,Ad Aertsen？,Arvind Kumar

Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia

Javier Macia？,Romilde Manzoni？,Núria Conde？,Arturo Urrios？,Eulàlia de Nadal？,Ricard Solé？,Francesc Posas

Control of βAR- and N-methyl-D-aspartate (NMDA) Receptor-Dependent cAMP Dynamics in Hippocampal Neurons

Andrew Chay？,Ilaria Zamparo？,Andreas Koschinski？,Manuela Zaccolo？,Kim T. Blackwell

Radial Frequency Analysis of Contour Shapes in the Visual Cortex

Viljami R. Salmela？,Linda Henriksson？,Simo Vanni

Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories

Harendra Guturu？,Sandeep Chinchali？,Shoa L. Clarke？,Gill Bejerano

MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression

Steven W. Paugh？,David R. Coss？,Ju Bao？,Lucas T. Laudermilk？,Christy R. Grace？,Antonio M. Ferreira？,M. Brett Waddell？,Granger Ridout？,Deanna Naeve？,Michael Leuze

Persistent Chaos of Measles Epidemics in the Prevaccination United States Caused by a Small Change in Seasonal Transmission Patterns

Benjamin D. Dalziel？,Ottar N. Bj？rnstad？,Willem G. van Panhuis？,Donald S. Burke？,C. Jessica E. Metcalf？,Bryan T. Grenfell

Ensemble Tractography

Hiromasa Takemura？,Cesar F. Caiafa？,Brian A. Wandell？,Franco Pestilli

The Emotional Gatekeeper: A Computational Model of Attentional Selection and Suppression through the Pathway from the Amygdala to the Inhibitory Thalamic Reticular Nucleus

Yohan J. John？,Basilis Zikopoulos？,Daniel Bullock？,Helen Barbas

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