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Table of Contents: July 2017

The ubiquitous hyaluronan sugar binds to its native CD44 receptor, mediating cell-environment interactions. Hyaluronan can bind CD44 in three well-defined binding modes, each characterized by a pair of spatially separated arginine residues. The image shows one of the binding modes discovered using simulation techniques. Each mode might play a different functional role, e.g. in aggregation kinetics.Vuorio et al.

Image Credit: Vuorio et al.

Research Articles

PCSF: An R-package for network-based interpretation of high-throughput data

Murodzhon Akhmedov, Amanda Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee

A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium

Oliver J. Maclaren, Aimée Parker, Carmen Pin, Simon R. Carding, Alastair J. M. Watson, Alexander G. Fletcher, Helen M. Byrne, Philip K. Maini

Dissociating error-based and reinforcement-based loss functions during sensorimotor learning

Joshua G. A. Cashaback, Heather R. McGregor, Ayman Mohatarem, Paul L. Gribble

Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors

Saeed Omidi, Mihaela Zavolan, Mikhail Pachkov, Jeremie Breda, Severin Berger, Erik van Nimwegen

Upregulation of an inward rectifying K+ channel can rescue slow Ca2+ oscillations in K(ATP) channel deficient pancreatic islets

Vehpi Yildirim, Suryakiran Vadrevu, Benjamin Thompson, Leslie S. Satin, Richard Bertram

Growth of bacteria in 3-d colonies

Xinxian Shao, Andrew Mugler, Justin Kim, Ha Jun Jeong, Bruce R. Levin, Ilya Nemenman

Recurrently connected and localized neuronal communities initiate coordinated spontaneous activity in neuronal networks

Davide Lonardoni, Hayder Amin, Stefano Di Marco, Alessandro Maccione, Luca Berdondini, Thierry Nieus

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Peter Eastman, Jason Swails, John D. Chodera, Robert T. McGibbon, Yutong Zhao, Kyle A. Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks, Vijay S. Pande

Spatial dynamics and control of a crop pathogen with mixed-mode transmission

Christopher Finn McQuaid, Frank van den Bosch, Anna Szyniszewska, Titus Alicai, Anthony Pariyo, Patrick Chiza Chikoti, Christopher Aidan Gilligan

Adjudicating between face-coding models with individual-face fMRI responses

Johan D. Carlin, Nikolaus Kriegeskorte

Reconstructing the regulatory circuit of cell fate determination in yeast mating response

Bin Shao, Haiyu Yuan, Rongfei Zhang, Xuan Wang, Shuwen Zhang, Qi Ouyang, Nan Hao, Chunxiong Luo

β-adrenergic signaling broadly contributes to LTP induction

Joanna Jȩdrzejewska-Szmek, Vincent Luczak, Ted Abel, Kim T Blackwell

A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation

Warren D. Anderson, Danielle DeCicco, James S. Schwaber, Rajanikanth Vadigepalli

Advances in using Internet searches to track dengue

Shihao Yang, Samuel C. Kou, Fred Lu, John S. Brownstein, Nicholas Brooke, Mauricio Santillana

Effect of depth information on multiple-object tracking in three dimensions: A probabilistic perspective

James R. H. Cooke, Arjan C. ter Horst, Robert J. van Beers, W. Pieter Medendorp

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume J. Filion, Marc A. Marti-Renom

CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets

Yang Li, Alexis A. Jourdain, Sarah E. Calvo, Jun S. Liu, Vamsi K. Mootha

Stress-induced mutagenesis: Stress diversity facilitates the persistence of mutator genes

Marta Lukačišinová, Sebastian Novak, Tiago Paixão

Atomistic fingerprint of hyaluronan–CD44 binding

Joni Vuorio, Ilpo Vattulainen, Hector Martinez-Seara

Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models

Connor Sharp, James Bray, Nicholas G. Housden, Martin C. J. Maiden, Colin Kleanthous

A curated genome-scale metabolic model of Bordetella pertussis metabolism

Nick Fyson, Jerry King, Thomas Belcher, Andrew Preston, Caroline Colijn

Deciphering the regulation of P2X4 receptor channel gating by ivermectin using Markov models

Laurent Mackay, Hana Zemkova, Stanko S. Stojilkovic, Arthur Sherman, Anmar Khadra

A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part I, experimental analysis

Mathieu Bottier, Sylvain Blanchon, Gabriel Pelle, Emilie Bequignon, Daniel Isabey, André Coste, Estelle Escudier, James B. Grotberg, Jean-François Papon, Marcel Filoche, Bruno Louis

Related Articles

  1. A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part II, modeling

A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part II, modeling

Mathieu Bottier, Marta Peña Fernández, Gabriel Pelle, Daniel Isabey, Bruno Louis, James B. Grotberg, Marcel Filoche

Related Articles

  1. A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part I, experimental analysis

Cooperative stochastic binding and unbinding explain synaptic size dynamics and statistics

Aseel Shomar, Lukas Geyrhofer, Noam E. Ziv, Naama Brenner

Hybrid modeling and prediction of dynamical systems

Franz Hamilton, Alun L. Lloyd, Kevin B. Flores

Inverse stochastic resonance in networks of spiking neurons

Muhammet Uzuntarla, Ernest Barreto, Joaquin J. Torres

Noise, multisensory integration, and previous response in perceptual disambiguation

Cesare V. Parise, Marc O. Ernst

Temporal specificity of the initial adaptive response in motor adaptation

Wilsaan M. Joiner, Gary C. Sing, Maurice A. Smith

Inherent limitations of probabilistic models for protein-DNA binding specificity

Shuxiang Ruan, Gary D. Stormo

Cannabinoids disrupt memory encoding by functionally isolating hippocampal CA1 from CA3

Roman A. Sandler, Dustin Fetterhoff, Robert E. Hampson, Sam A. Deadwyler, Vasilis Z. Marmarelis

Flux balance analysis predicts Warburg-like effects of mouse hepatocyte deficient in miR-122a

Hua-Qing Wu, Mei-Ling Cheng, Jin-Mei Lai, Hsuan-Hui Wu, Meng-Chun Chen, Wen-Huan Liu, Wu-Hsiung Wu, Peter Mu-Hsin Chang, Chi-Ying F. Huang, Ann-Ping Tsou, Ming-Shi Shiao, Feng-Sheng Wang

Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires

Mikhail V. Pogorelyy, Yuval Elhanati, Quentin Marcou, Anastasiia L. Sycheva, Ekaterina A. Komech, Vadim I. Nazarov, Olga V. Britanova, Dmitriy M. Chudakov, Ilgar Z. Mamedov, Yury B. Lebedev, Thierry Mora, Aleksandra M. Walczak

Rapid target foraging with reach or gaze: The hand looks further ahead than the eye

Jonathan S. Diamond, Daniel M. Wolpert, J. Randall Flanagan

Combination therapeutics of Nilotinib and radiation in acute lymphoblastic leukemia as an effective method against drug-resistance

Kamran Kaveh, Yutaka Takahashi, Michael A. Farrar, Guy Storme, Marcucci Guido, Jamie Piepenburg, Jackson Penning, Jasmine Foo, Kevin Z. Leder, Susanta K. Hui

Classification and analysis of a large collection of in vivo bioassay descriptions

Magdalena Zwierzyna, John P. Overington

Quantifying critical states of complex diseases using single-sample dynamic network biomarkers

Xiaoping Liu, Xiao Chang, Rui Liu, Xiangtian Yu, Luonan Chen, Kazuyuki Aihara

Epistasis in genomic and survival data of cancer patients

Dariusz Matlak, Ewa Szczurek

Speciation trajectories in recombining bacterial species

Pekka Marttinen, William P. Hanage

Universal features of dendrites through centripetal branch ordering

Alexandra Vormberg, Felix Effenberger, Julia Muellerleile, Hermann Cuntz

Expanding signaling-molecule wavefront model of cell polarization in the Drosophila wing primordium

Juliana C. Wortman, Marcos Nahmad, Peng Cheng Zhang, Arthur D. Lander, Clare C. Yu