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Table of Contents

August 2020

Hypoxia within solid tumors resulting from increased oxygen consumption and abnormal vascularization limits the effectiveness of cancer therapies. This image depicts the oxygen gradient of a hypoxic tumor growing in a vascularized bed interjacent of arterial and venous nodes. Here, the tumor has altered the vasculature, reducing venular oxygen transport. Using these models of vascular oxygen transport, Belcher et al explored how the tumor oxygenation potential of hemoglobin-based oxygen carriers (HBOCs) can differ between mice and humans. Specifically, they estimated which clinically measurable properties of the tumor may help translate HBOC facilitated tumor oxygenation from murine models to the clinic.

Image Credit: Donald Belcher, The Ohio State University

Education

Ten simple rules to increase computational skills among biologists with Code Clubs

Ada K. Hagan, Nicholas A. Lesniak, Marcy J. Balunas, Lucas Bishop, William L. Close, Matthew D. Doherty, Amanda G. Elmore, Kaitlin J. Flynn, Geoffrey D. Hannigan, Charlie C. Koumpouras, Matthew L. Jenior, Ariangela J. Kozik, Kathryn McBride, Samara B. Rifkin, Joshua M. A. Stough, Kelly L. Sovacool, Marc A. Sze, Sarah Tomkovich, Begum D. Topcuoglu, Patrick D. Schloss

Perspective

Ten simple rules to power drug discovery with data science

Enrico Ferrero, Sophie Brachat, Jeremy L. Jenkins, Philippe Marc, Peter Skewes-Cox, Robert C. Altshuler, Caroline Gubser Keller, Audrey Kauffmann, Erik K. Sassaman, Jason M. Laramie, Birgit Schoeberl, Mark L. Borowsky, Nikolaus Stiefl

Research Articles

Multiplexing information flow through dynamic signalling systems

Giorgos Minas, Dan J. Woodcock, Louise Ashall, Claire V. Harper, Michael R. H. White, David A. Rand

Task-evoked activity quenches neural correlations and variability across cortical areas

Takuya Ito, Scott L. Brincat, Markus Siegel, Ravi D. Mill, Biyu J. He, Earl K. Miller, Horacio G. Rotstein, Michael W. Cole

Combining hypoxia-activated prodrugs and radiotherapy in silico: Impact of treatment scheduling and the intra-tumoural oxygen landscape

Sara Hamis, Mohammad Kohandel, Ludwig J. Dubois, Ala Yaromina, Philippe Lambin, Gibin G. Powathil

Optimising efficacy of antibiotics against systemic infection by varying dosage quantities and times

Andy Hoyle, David Cairns, Iona Paterson, Stuart McMillan, Gabriela Ochoa, Andrew P. Desbois

Flexible neural connectivity under constraints on total connection strength

Gabriel Koch Ocker, Michael A. Buice

Predicting precision grip grasp locations on three-dimensional objects

Lina K. Klein, Guido Maiello, Vivian C. Paulun, Roland W. Fleming

Effect of magnitude and variability of energy of activation in multisite ultrasensitive biochemical processes

Leonila Lagunes, Lee Bardwell, German A. Enciso

A machine learning and network framework to discover new indications for small molecules

Coryandar Gilvary, Jamal Elkhader, Neel Madhukar, Claire Henchcliffe, Marcus D. Goncalves, Olivier Elemento

Presynaptic inhibition rapidly stabilises recurrent excitation in the face of plasticity

Laura Bella Naumann, Henning Sprekeler

Achieving stable dynamics in neural circuits

Leo Kozachkov, Mikael Lundqvist, Jean-Jacques Slotine, Earl K. Miller

Reliable estimation of membrane curvature for cryo-electron tomography

Maria Salfer, Javier F. Collado, Wolfgang Baumeister, Rubén Fernández-Busnadiego, Antonio Martínez-Sánchez

Facilitating the propagation of spiking activity in feedforward networks by including feedback

Hedyeh Rezaei, Ad Aertsen, Arvind Kumar, Alireza Valizadeh

Order matters: How covert value updating during sequential option sampling shapes economic preference

Chen Hu, Philippe Domenech, Mathias Pessiglione

Engineering recurrent neural networks from task-relevant manifolds and dynamics

Eli Pollock, Mehrdad Jazayeri

Inferring the ancestry of parents and grandparents from genetic data

Jingwen Pei, Yiming Zhang, Rasmus Nielsen, Yufeng Wu

Information transmission from NFkB signaling dynamics to gene expression

Alok Maity, Roy Wollman

Machine Learning based histology phenotyping to investigate the epidemiologic and genetic basis of adipocyte morphology and cardiometabolic traits

Craig A. Glastonbury, Sara L. Pulit, Julius Honecker, Jenny C. Censin, Samantha Laber, Hanieh Yaghootkar, Nilufer Rahmioglu, Emilie Pastel, Katerina Kos, Andrew Pitt, Michelle Hudson, Christoffer Nellåker, Nicola L. Beer, Hans Hauner, Christian M. Becker, Krina T. Zondervan, Timothy M. Frayling, Melina Claussnitzer, Cecilia M. Lindgren

A computational model of induced pluripotent stem-cell derived cardiomyocytes for high throughput risk stratification of KCNQ1 genetic variants

Divya C. Kernik, Pei-Chi Yang, Junko Kurokawa, Joseph C. Wu, Colleen E. Clancy

Drug-target binding quantitatively predicts optimal antibiotic dose levels in quinolones

Fabrizio Clarelli, Adam Palmer, Bhupender Singh, Merete Storflor, Silje Lauksund, Ted Cohen, Sören Abel, Pia Abel zur Wiesch

Vector genetics, insecticide resistance and gene drives: An agent-based modeling approach to evaluate malaria transmission and elimination

Prashanth Selvaraj, Edward A. Wenger, Daniel Bridenbecker, Nikolai Windbichler, Jonathan R. Russell, Jaline Gerardin, Caitlin A. Bever, Milen Nikolov

In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target

Isaias Lans, Ernesto Anoz-Carbonell, Karen Palacio-Rodríguez, José Antonio Aínsa, Milagros Medina, Pilar Cossio

Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4

Wai Kit Ong, Dylan K. Courtney, Shu Pan, Ramon Bonela Andrade, Patricia J. Kiley, Brian F. Pfleger, Jennifer L. Reed

Deconvolving the contributions of cell-type heterogeneity on cortical gene expression

Ellis Patrick, Mariko Taga, Ayla Ergun, Bernard Ng, William Casazza, Maria Cimpean, Christina Yung, Julie A. Schneider, David A. Bennett, Chris Gaiteri, Philip L. De Jager, Elizabeth M. Bradshaw, Sara Mostafavi

Real-time estimation of disease activity in emerging outbreaks using internet search information

Emily L. Aiken, Sarah F. McGough, Maimuna S. Majumder, Gal Wachtel, Andre T. Nguyen, Cecile Viboud, Mauricio Santillana

A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis

Amrit Dhar, Duncan K. Ralph, Vladimir N. Minin, Frederick A. Matsen IV

Modeling time-varying brain networks with a self-tuning optimized Kalman filter

D. Pascucci, M. Rubega, G. Plomp

Mathematical modelling reveals cellular dynamics within tumour spheroids

Joshua A. Bull, Franziska Mech, Tom Quaiser, Sarah L. Waters, Helen M. Byrne

JBrowse Connect: A server API to connect JBrowse instances and users

Eric Yao, Robert Buels, Lincoln Stein, Taner Z. Sen, Ian Holmes

Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence

Chen Liao, Tong Wang, Sergei Maslov, Joao B. Xavier

Mathematical model and tool to explore shorter multi-drug therapy options for active pulmonary tuberculosis

John Fors, Natasha Strydom, William S. Fox, Ron J. Keizer, Radojka M. Savic

Visual perception of liquids: Insights from deep neural networks

Jan Jaap R. van Assen, Shin’ya Nishida, Roland W. Fleming

Dynamic estimation of auditory temporal response functions via state-space models with Gaussian mixture process noise

Sina Miran, Alessandro Presacco, Jonathan Z. Simon, Michael C. Fu, Steven I. Marcus, Behtash Babadi

Tumor vascular status controls oxygen delivery facilitated by infused polymerized hemoglobins with varying oxygen affinity

Donald A. Belcher, Alfredo Lucas, Pedro Cabrales, Andre F. Palmer

Epithelial organ shape is generated by patterned actomyosin contractility and maintained by the extracellular matrix

Ali Nematbakhsh, Megan Levis, Nilay Kumar, Weitao Chen, Jeremiah J. Zartman, Mark Alber

Template-based mapping of dynamic motifs in tissue morphogenesis

Tomer Stern, Stanislav Y. Shvartsman, Eric F. Wieschaus

Managing disease outbreaks: The importance of vector mobility and spatially heterogeneous control

Jeffery Demers, Sharon Bewick, Folashade Agusto, Kevin A. Caillouët, William F. Fagan, Suzanne L. Robertson

Simulating flow induced migration in vascular remodelling

Ashkan Tabibian, Siavash Ghaffari, Diego A. Vargas, Hans Van Oosterwyck, Elizabeth A. V. Jones

A novel single-cell based method for breast cancer prognosis

Xiaomei Li, Lin Liu, Gregory J. Goodall, Andreas Schreiber, Taosheng Xu, Jiuyong Li, Thuc D. Le

Cell signaling model for arterial mechanobiology

Linda Irons, Jay D. Humphrey

Firing rate homeostasis counteracts changes in stability of recurrent neural networks caused by synapse loss in Alzheimer’s disease

Claudia Bachmann, Tom Tetzlaff, Renato Duarte, Abigail Morrison

A steady-state model of microbial acclimation to substrate limitation

John R. Casey, Michael J. Follows

Buildup and bistability in auditory streaming as an evidence accumulation process with saturation

Quynh-Anh Nguyen, John Rinzel, Rodica Curtu

Computational estimates of mechanical constraints on cell migration through the extracellular matrix

Ondrej Maxian, Alex Mogilner, Wanda Strychalski

Modeling microbial metabolic trade-offs in a chemostat

Zhiyuan Li, Bo Liu, Sophia Hsin-Jung Li, Christopher G. King, Zemer Gitai, Ned S. Wingreen

Computer-guided binding mode identification and affinity improvement of an LRR protein binder without structure determination

Yoonjoo Choi, Sukyo Jeong, Jung-Min Choi, Christian Ndong, Karl E. Griswold, Chris Bailey-Kellogg, Hak-Sung Kim