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Table of Contents

June 2019

Predicted fold of an RNA chain as an Eterna videogame player changes its sequence to eventually arrive at a target fold.

Image Credit: Eterna

Editorial

Ten simple rules for successfully hosting an intern at a scientific software company

Kristine Briedis, Yi-Shiou Chen, Scott Markel

Education Articles

Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors

Yingqian Ada Zhan, Charles Gregory Wray, Sandeep Namburi, Spencer T. Glantz, Reinhard Laubenbacher, Jeffrey H. Chuang

Ten quick tips for effective dimensionality reduction

Lan Huong Nguyen, Susan Holmes

Problem-based learning in clinical bioinformatics education: Does it help to create communities of practice?

Angela C. Davies, Diane Harris, Amanda Banks-Gatenby, Andy Brass

From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training

Annette McGrath, Katherine Champ, Catherine A. Shang, Ellen van Dam, Cath Brooksbank, Sarah L. Morgan

Perspective

Telling ecological networks apart by their structure: A computational challenge

Matthew J. Michalska-Smith, Stefano Allesina

Reviews

Modern technologies and algorithms for scaffolding assembled genomes

Jay Ghurye, Mihai Pop

Protein ensembles link genotype to phenotype

Ruth Nussinov, Chung-Jung Tsai, Hyunbum Jang

Neural correlates of sparse coding and dimensionality reduction

Michael Beyeler, Emily L. Rounds, Kristofor D. Carlson, Nikil Dutt, Jeffrey L. Krichmar

Research Articles

Evolution of interface binding strengths in simplified model of protein quaternary structure

Alexander S. Leonard, Sebastian E. Ahnert

Exploring E-cadherin-peptidomimetics interaction using NMR and computational studies

Monica Civera, Francesca Vasile, Donatella Potenza, Cinzia Colombo, Sara Parente, Chiara Vettraino, Tommaso Prosdocimi, Emilio Parisini, Laura Belvisi

Mathematical modelling reveals unexpected inheritance and variability patterns of cell cycle parameters in mammalian cells

Marzena Mura, Céline Feillet, Roberto Bertolusso, Franck Delaunay, Marek Kimmel

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Chuankai Cheng, Edward J. O’Brien, Douglas McCloskey, Jose Utrilla, Connor Olson, Ryan A. LaCroix, Troy E. Sandberg, Adam M. Feist, Bernhard O. Palsson, Zachary A. King

Multiscale model of integrin adhesion assembly

Tamara C. Bidone, Austin V. Skeeters, Patrick W. Oakes, Gregory A. Voth

Phenotypic heterogeneity and evolution of melanoma cells associated with targeted therapy resistance

Yapeng Su, Marcus Bintz, Yezi Yang, Lidia Robert, Alphonsus H. C. Ng, Victoria Liu, Antoni Ribas, James R. Heath, Wei Wei

Charting pathways to climate change mitigation in a coupled socio-climate model

Thomas M. Bury, Chris T. Bauch, Madhur Anand

The breadth of HIV-1 neutralizing antibodies depends on the conservation of key sites in their epitopes

Hongjun Bai, Yifan Li, Nelson L. Michael, Merlin L. Robb, Morgane Rolland

Dynamic properties of internal noise probed by modulating binocular rivalry

Daniel H. Baker, Bruno Richard

Horizontal transfer between loose compartments stabilizes replication of fragmented ribozymes

Atsushi Kamimura, Yoshiya J. Matsubara, Kunihiko Kaneko, Nobuto Takeuchi

A neural field model for color perception unifying assimilation and contrast

Anna Song, Olivier Faugeras, Romain Veltz

How single neuron properties shape chaotic dynamics and signal transmission in random neural networks

Samuel P. Muscinelli, Wulfram Gerstner, Tilo Schwalger

Models that learn how humans learn: The case of decision-making and its disorders

Amir Dezfouli, Kristi Griffiths, Fabio Ramos, Peter Dayan, Bernard W. Balleine

Disentangling juxtacrine from paracrine signalling in dynamic tissue

Hiroshi Momiji, Kirsty L. Hassall, Karen Featherstone, Anne V. McNamara, Amanda L. Patist, David G. Spiller, Helen C. Christian, Michael R. H. White, Julian R. E. Davis, Bärbel F. Finkenstädt, David A. Rand

Integrative modeling of the HIV-1 ribonucleoprotein complex

David S. Goodsell, Andrew Jewett, Arthur J. Olson, Stefano Forli

Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome

Kymberleigh A. Pagel, Danny Antaki, AoJie Lian, Matthew Mort, David N. Cooper, Jonathan Sebat, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac

A multi-scale model of gas transport in the lung to study heterogeneous lung ventilation during the multiple-breath washout test

David Hasler, Pinelopi Anagnostopoulou, Sylvia Nyilas, Philipp Latzin, Johannes Schittny, Dominik Obrist

Hierarchical Bayesian inference for concurrent model fitting and comparison for group studies

Payam Piray, Amir Dezfouli, Tom Heskes, Michael J. Frank, Nathaniel D. Daw

Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes

Claire Bomkamp, Shreejoy J. Tripathy, Carolina Bengtsson Gonzales, Jens Hjerling-Leffler, Ann Marie Craig, Paul Pavlidis

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)

Benedict Borer, Meriç Ataman, Vassily Hatzimanikatis, Dani Or

Coupling water fluxes with cell wall mechanics in a multicellular model of plant development

Ibrahim Cheddadi, Michel Génard, Nadia Bertin, Christophe Godin

Modelling the transport of fluid through heterogeneous, whole tumours in silico

Paul W. Sweeney, Angela d’Esposito, Simon Walker-Samuel, Rebecca J. Shipley

Resurgent Na+ Current Offers Noise Modulation in Bursting Neurons

Sharmila Venugopal, Soju Seki, David H. Terman, Antonios Pantazis, Riccardo Olcese, Martina Wiedau-Pazos, Scott H. Chandler

Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa

Anthony Hauser, Katharina Kusejko, Leigh F. Johnson, Gilles Wandeler, Julien Riou, Fardo Goldstein, Matthias Egger, Roger D. Kouyos

Learning to use past evidence in a sophisticated world model

Sanjeevan Ahilan, Rebecca B. Solomon, Yannick-André Breton, Kent Conover, Ritwik K. Niyogi, Peter Shizgal, Peter Dayan

Open collaborative writing with Manubot

Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter

A neural network model predicts community-level signaling states in a diverse microbial community

Kalinga Pavan T. Silva, James Q. Boedicker

A new framework for assessing subject-specific whole brain circulation and perfusion using MRI-based measurements and a multi-scale continuous flow model

Erlend Hodneland, Erik Hanson, Ove Sævareid, Geir Nævdal, Arvid Lundervold, Veronika Šoltészová, Antonella Z. Munthe-Kaas, Andreas Deistung, Jürgen R. Reichenbach, Jan M. Nordbotten

Model-inferred mechanisms of liver function from magnetic resonance imaging data: Validation and variation across a clinically relevant cohort

Mikael F. Forsgren, Markus Karlsson, Olof Dahlqvist Leinhard, Nils Dahlström, Bengt Norén, Thobias Romu, Simone Ignatova, Mattias Ekstedt, Stergios Kechagias, Peter Lundberg, Gunnar Cedersund

Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations

Hanne Hoitzing, Payam A. Gammage, Lindsey Van Haute, Michal Minczuk, Iain G. Johnston, Nick S. Jones

Optimization of surgical intervention outside the epileptogenic zone in the Virtual Epileptic Patient (VEP)

Sora An, Fabrice Bartolomei, Maxime Guye, Viktor Jirsa

Predicting gastrointestinal drug effects using contextualized metabolic models

Marouen Ben Guebila, Ines Thiele

Drosophila melanogaster grooming possesses syntax with distinct rules at different temporal scales

Joshua M. Mueller, Primoz Ravbar, Julie H. Simpson, Jean M. Carlson

Augmenting subnetwork inference with information extracted from the scientific literature

Sid Kiblawi, Deborah Chasman, Amanda Henning, Eunju Park, Hoifung Poon, Michael Gould, Paul Ahlquist, Mark Craven

Modeling the temporal dynamics of the gut microbial community in adults and infants

Liat Shenhav, Ori Furman, Leah Briscoe, Mike Thompson, Justin D. Silverman, Itzhak Mizrahi, Eran Halperin

EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame

Rohan V. Koodli, Benjamin Keep, Katherine R. Coppess, Fernando Portela, Eterna participants, Rhiju Das

Evidence accumulation is biased by motivation: A computational account

Filip Gesiarz, Donal Cahill, Tali Sharot

Corrections

Correction: Geospatial characteristics of measles transmission in China during 2005−2014

Wan Yang, Liang Wen, Shen-Long Li, Kai Chen, Wen-Yi Zhang, Jeffrey Shaman

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