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Table of Contents

April 2023

Artwork composed of the spectrogram of a bonobo call and photographs of three adult bonobo individuals from La Vallée des Singes (France). Arnaud et al 2023

Image Credit: François Pellegrino


Ten simple rules for working with other people’s code

Charlie Pilgrim, Paul Kent, Kasra Hosseini, Ed Chalstrey


Bridging the gap between mechanistic biological models and machine learning surrogates

Ioana M. Gherman, Zahraa S. Abdallah, Wei Pang, Thomas E. Gorochowski, Claire S. Grierson, Lucia Marucci

Research Articles

Applying a GAN-based classifier to improve transcriptome-based prognostication in breast cancer

Cristiano Guttà, Christoph Morhard, Markus Rehm

The contribution of the basal ganglia and cerebellum to motor learning: A neuro-computational approach

Javier Baladron, Julien Vitay, Torsten Fietzek, Fred H. Hamker

Uncovering the organization of neural circuits with Generalized Phase Locking Analysis

Shervin Safavi, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F. Ramirez-Villegas, Nikos K. Logothetis, Michel Besserve

Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies

Carolin Zitzmann, Christopher Dächert, Bianca Schmid, Hilde van der Schaar, Martijn van Hemert, Alan S. Perelson, Frank J. M. van Kuppeveld, Ralf Bartenschlager, Marco Binder, Lars Kaderali

GenoVi, an open-source automated circular genome visualizer for bacteria and archaea

Andrés Cumsille, Roberto E. Durán, Andrea Rodríguez-Delherbe, Vicente Saona-Urmeneta, Beatriz Cámara, Michael Seeger, Mauricio Araya, Nicolás Jara, Carlos Buil-Aranda

Neural spiking for causal inference and learning

Benjamin James Lansdell, Konrad Paul Kording

Inferring assembly-curving trends of bacterial micro-compartment shell hexamers from crystal structure arrangements

Luis F. Garcia-Alles, Miguel Fuentes-Cabrera, Gilles Truan, David Reguera

Delayed skeletal muscle repair following inflammatory damage in simulated agent-based models of muscle regeneration

Stephanie Khuu, Justin W. Fernandez, Geoffrey G. Handsfield

Increased A-to-I RNA editing in atherosclerosis and cardiomyopathies

Tomer D. Mann, Eli Kopel, Eli Eisenberg, Erez Y. Levanon

Diverse role of NMDA receptors for dendritic integration of neural dynamics

Yuanhong Tang, Xingyu Zhang, Lingling An, Zhaofei Yu, Jian K. Liu

In-silico EEG biomarkers of reduced inhibition in human cortical microcircuits in depression

Frank Mazza, Alexandre Guet-McCreight, Taufik A. Valiante, John D. Griffiths, Etay Hay

Purely STDP-based assembly dynamics: Stability, learning, overlaps, drift and aging

Paul Manz, Raoul-Martin Memmesheimer

Gate-based quantum computing for protein design

Mohammad Hassan Khatami, Udson C. Mendes, Nathan Wiebe, Philip M. Kim

Complex spatiotemporal oscillations emerge from transverse instabilities in large-scale brain networks

Pau Clusella, Gustavo Deco, Morten L. Kringelbach, Giulio Ruffini, Jordi Garcia-Ojalvo

Toward an optimal contraception dosing strategy

Brenda Lyn A. Gavina, Aurelio A. de los Reyes V, Mette S. Olufsen, Suzanne Lenhart, Johnny T. Ottesen

A framework for deriving analytic steady states of biochemical reaction networks

Bryan S. Hernandez, Patrick Vincent N. Lubenia, Matthew D. Johnston, Jae Kyoung Kim

High rifampicin peak plasma concentrations accelerate the slow phase of bacterial decline in tuberculosis patients: Evidence for heteroresistance

Antal Martinecz, Martin J. Boeree, Andreas H. Diacon, Rodney Dawson, Colin Hemez, Rob E. Aarnoutse, Pia Abel zur Wiesch

Improving the workflow to crack Small, Unbalanced, Noisy, but Genuine (SUNG) datasets in bioacoustics: The case of bonobo calls

Vincent Arnaud, François Pellegrino, Sumir Keenan, Xavier St-Gelais, Nicolas Mathevon, Florence Levréro, Christophe Coupé

Recurrent predictive coding models for associative memory employing covariance learning

Mufeng Tang, Tommaso Salvatori, Beren Millidge, Yuhang Song, Thomas Lukasiewicz, Rafal Bogacz

Dual contribution of ASIC1a channels in the spinal processing of pain information by deep projection neurons revealed by computational modeling

Magda Chafaï, Ariane Delrocq, Perrine Inquimbert, Ludivine Pidoux, Kevin Delanoe, Maurizio Toft, Frederic Brau, Eric Lingueglia, Romain Veltz, Emmanuel Deval

A combined experimental-computational approach uncovers a role for the Golgi matrix protein Giantin in breast cancer progression

Salim Ghannoum, Damiano Fantini, Muhammad Zahoor, Veronika Reiterer, Santosh Phuyal, Waldir Leoncio Netto, Øystein Sørensen, Arvind Iyer, Debarka Sengupta, Lina Prasmickaite, Gunhild Mari Mælandsmo, Alvaro Köhn-Luque, Hesso Farhan

How synaptic strength, short-term plasticity, and input synchrony contribute to neuronal spike output

Moritz O. Buchholz, Alexandra Gastone Guilabert, Benjamin Ehret, Gregor F. P. Schuhknecht

Rare-event sampling analysis uncovers the fitness landscape of the genetic code

Yuji Omachi, Nen Saito, Chikara Furusawa

A fast machine-learning-guided primer design pipeline for selective whole genome amplification

Jane A. Dwivedi-Yu, Zachary J. Oppler, Matthew W. Mitchell, Yun S. Song, Dustin Brisson

Calibrating agent-based models to tumor images using representation learning

Colin G. Cess, Stacey D. Finley

Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference

Aidan B. Estelle, August George, Elisar J. Barbar, Daniel M. Zuckerman

Bioinspired figure-ground discrimination via visual motion smoothing

Zhihua Wu, Aike Guo

A multispecies framework for modeling adaptive immunity and immunotherapy in cancer

Timothy Qi, Benjamin G. Vincent, Yanguang Cao

The functional logic of odor information processing in the Drosophila antennal lobe

Aurel A. Lazar, Tingkai Liu, Chung-Heng Yeh

MitoTNT: Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data

Zichen Wang, Parth Natekar, Challana Tea, Sharon Tamir, Hiroyuki Hakozaki, Johannes Schöneberg

Minor variations in multicellular life cycles have major effects on adaptation

Hanna Isaksson, Åke Brännström, Eric Libby

MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication

Tarun Kumar, Ramanathan Sethuraman, Sanga Mitra, Balaraman Ravindran, Manikandan Narayanan

Efficient coding of natural scenes improves neural system identification

Yongrong Qiu, David A. Klindt, Klaudia P. Szatko, Dominic Gonschorek, Larissa Hoefling, Timm Schubert, Laura Busse, Matthias Bethge, Thomas Euler

Shape-driven deep neural networks for fast acquisition of aortic 3D pressure and velocity flow fields

Endrit Pajaziti, Javier Montalt-Tordera, Claudio Capelli, Raphaël Sivera, Emilie Sauvage, Michael Quail, Silvia Schievano, Vivek Muthurangu

Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease

Natalia Ostrowska, Michael Feig, Joanna Trylska

Fidelity of hyperbolic space for Bayesian phylogenetic inference

Matthew Macaulay, Aaron Darling, Mathieu Fourment

Model certainty in cellular network-driven processes with missing data

Michael W. Irvin, Arvind Ramanathan, Carlos F. Lopez

Network analysis of toxin production in Clostridioides difficile identifies key metabolic dependencies

Deborah A. Powers, Matthew L. Jenior, Glynis L. Kolling, Jason A. Papin

Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides

Alīna Reķēna, Marina J. Pinheiro, Nemailla Bonturi, Isma Belouah, Eliise Tammekivi, Koit Herodes, Eduard J. Kerkhoven, Petri-Jaan Lahtvee

Personalized prediction of the secondary oocytes number after ovarian stimulation: A machine learning model based on clinical and genetic data

Krystian Zieliński, Sebastian Pukszta, Małgorzata Mickiewicz, Marta Kotlarz, Piotr Wygocki, Marcin Zieleń, Dominika Drzewiecka, Damian Drzyzga, Anna Kloska, Joanna Jakóbkiewicz-Banecka

Fusing an agent-based model of mosquito population dynamics with a statistical reconstruction of spatio-temporal abundance patterns

Sean M. Cavany, Guido España, Alun L. Lloyd, Gonzalo M. Vazquez-Prokopec, Helvio Astete, Lance A. Waller, Uriel Kitron, Thomas W. Scott, Amy C. Morrison, Robert C. Reiner Jr, T. Alex Perkins

Dopamine depletion leads to pathological synchronization of distinct basal ganglia loops in the beta band

Andrea Ortone, Alberto Arturo Vergani, Mahboubeh Ahmadipour, Riccardo Mannella, Alberto Mazzoni

A high-frequency mobility big-data reveals how COVID-19 spread across professions, locations and age groups

Chen Zhao, Jialu Zhang, Xiaoyue Hou, Chi Ho Yeung, An Zeng

The representational hierarchy in human and artificial visual systems in the presence of object-scene regularities

Stefania Bracci, Jakob Mraz, Astrid Zeman, Gaëlle Leys, Hans Op de Beeck