Ten simple rules for working with other people’s code

Charlie Pilgrim, Paul Kent, Kasra Hosseini, Ed Chalstrey

PLOS Computational Biology: published April 20, 2023 | https://doi.org/10.1371/journal.pcbi.1011031

Establishing effective cross-disciplinary collaboration: Combining simple rules for reproducible computational research, a good data management plan, and good research practice

Bogna Stawarczyk, Małgorzata Roos

PLOS Computational Biology: published April 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011052

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

PLOS Computational Biology: published April 20, 2023 | https://doi.org/10.1371/journal.pcbi.1010988

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

Cristiano Guttà, Christoph Morhard, Markus Rehm

PLOS Computational Biology: published April 3, 2023 | https://doi.org/10.1371/journal.pcbi.1011035

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

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

PLOS Computational Biology: published April 3, 2023 | https://doi.org/10.1371/journal.pcbi.1011024

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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

PLOS Computational Biology: published April 3, 2023 | https://doi.org/10.1371/journal.pcbi.1010983

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

PLOS Computational Biology: published April 4, 2023 | https://doi.org/10.1371/journal.pcbi.1010423

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

PLOS Computational Biology: published April 4, 2023 | https://doi.org/10.1371/journal.pcbi.1010998

Neural spiking for causal inference and learning

Benjamin James Lansdell, Konrad Paul Kording

PLOS Computational Biology: published April 4, 2023 | https://doi.org/10.1371/journal.pcbi.1011005

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

PLOS Computational Biology: published April 5, 2023 | https://doi.org/10.1371/journal.pcbi.1011038

Pleiotropy promotes the evolution of inducible immune responses in a model of host-pathogen coevolution

Reese A. Martin, Ann T. Tate

PLOS Computational Biology: published April 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010445

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

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

PLOS Computational Biology: published April 6, 2023 | https://doi.org/10.1371/journal.pcbi.1011042

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

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

PLOS Computational Biology: published April 10, 2023 | https://doi.org/10.1371/journal.pcbi.1010923

Diverse role of NMDA receptors for dendritic integration of neural dynamics

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

PLOS Computational Biology: published April 10, 2023 | https://doi.org/10.1371/journal.pcbi.1011019

Ceramide-1-phosphate transfer protein enhances lipid transport by disrupting hydrophobic lipid–membrane contacts

Julia R. Rogers, Phillip L. Geissler

PLOS Computational Biology: published April 10, 2023 | https://doi.org/10.1371/journal.pcbi.1010992

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

PLOS Computational Biology: published April 10, 2023 | https://doi.org/10.1371/journal.pcbi.1010986

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

Paul Manz, Raoul-Martin Memmesheimer

PLOS Computational Biology: published April 12, 2023 | https://doi.org/10.1371/journal.pcbi.1011006

Identifying the engagement of a brain network during a targeted tDCS-fMRI experiment using a machine learning approach

Anant Shinde, Sovesh Mohapatra, Gottfried Schlaug

PLOS Computational Biology: published April 12, 2023 | https://doi.org/10.1371/journal.pcbi.1011012

Gate-based quantum computing for protein design

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

PLOS Computational Biology: published April 12, 2023 | https://doi.org/10.1371/journal.pcbi.1011033

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

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

PLOS Computational Biology: published April 12, 2023 | https://doi.org/10.1371/journal.pcbi.1010781

Toward an optimal contraception dosing strategy

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

PLOS Computational Biology: published April 13, 2023 | https://doi.org/10.1371/journal.pcbi.1010073

A framework for deriving analytic steady states of biochemical reaction networks

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

PLOS Computational Biology: published April 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011039

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

PLOS Computational Biology: published April 13, 2023 | https://doi.org/10.1371/journal.pcbi.1011000

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

PLOS Computational Biology: published April 13, 2023 | https://doi.org/10.1371/journal.pcbi.1010325

Recurrent predictive coding models for associative memory employing covariance learning

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

PLOS Computational Biology: published April 14, 2023 | https://doi.org/10.1371/journal.pcbi.1010719

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

PLOS Computational Biology: published April 17, 2023 | https://doi.org/10.1371/journal.pcbi.1010993

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

PLOS Computational Biology: published April 17, 2023 | https://doi.org/10.1371/journal.pcbi.1010995

Sequence similarity governs generalizability of de novo deep learning models for RNA secondary structure prediction

Xiangyun Qiu

PLOS Computational Biology: published April 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011047

Multi-view clustering by CPS-merge analysis with application to multimodal single-cell data

Lixiang Zhang, Lin Lin, Jia Li

PLOS Computational Biology: published April 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011044

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

PLOS Computational Biology: published April 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011046

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

Yuji Omachi, Nen Saito, Chikara Furusawa

PLOS Computational Biology: published April 17, 2023 | https://doi.org/10.1371/journal.pcbi.1011034

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

PLOS Computational Biology: published April 17, 2023 | https://doi.org/10.1371/journal.pcbi.1010137

Being noisy in a crowd: Differential selective pressure on gene expression noise in model gene regulatory networks

Nataša Puzović, Tanvi Madaan, Julien Y. Dutheil

PLOS Computational Biology: published April 20, 2023 | https://doi.org/10.1371/journal.pcbi.1010982

Calibrating agent-based models to tumor images using representation learning

Colin G. Cess, Stacey D. Finley

PLOS Computational Biology: published April 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011070

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

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

PLOS Computational Biology: published April 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011059

Bioinspired figure-ground discrimination via visual motion smoothing

Zhihua Wu, Aike Guo

PLOS Computational Biology: published April 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011077

A multispecies framework for modeling adaptive immunity and immunotherapy in cancer

Timothy Qi, Benjamin G. Vincent, Yanguang Cao

PLOS Computational Biology: published April 21, 2023 | https://doi.org/10.1371/journal.pcbi.1010976

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

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

PLOS Computational Biology: published April 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011043

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

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

PLOS Computational Biology: published April 21, 2023 | https://doi.org/10.1371/journal.pcbi.1011060

Minor variations in multicellular life cycles have major effects on adaptation

Hanna Isaksson, Åke Brännström, Eric Libby

PLOS Computational Biology: published April 21, 2023 | https://doi.org/10.1371/journal.pcbi.1010698

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

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

PLOS Computational Biology: published April 24, 2023 | https://doi.org/10.1371/journal.pcbi.1011022

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

PLOS Computational Biology: published April 24, 2023 | https://doi.org/10.1371/journal.pcbi.1011037

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

PLOS Computational Biology: published April 24, 2023 | https://doi.org/10.1371/journal.pcbi.1011055

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

Natalia Ostrowska, Michael Feig, Joanna Trylska

PLOS Computational Biology: published April 25, 2023 | https://doi.org/10.1371/journal.pcbi.1011054

Fidelity of hyperbolic space for Bayesian phylogenetic inference

Matthew Macaulay, Aaron Darling, Mathieu Fourment

PLOS Computational Biology: published April 26, 2023 | https://doi.org/10.1371/journal.pcbi.1011084

Model certainty in cellular network-driven processes with missing data

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

PLOS Computational Biology: published April 26, 2023 | https://doi.org/10.1371/journal.pcbi.1011004

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

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

PLOS Computational Biology: published April 26, 2023 | https://doi.org/10.1371/journal.pcbi.1011076

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

PLOS Computational Biology: published April 26, 2023 | https://doi.org/10.1371/journal.pcbi.1011009

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

PLOS Computational Biology: published April 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011020

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

PLOS Computational Biology: published April 27, 2023 | https://doi.org/10.1371/journal.pcbi.1010424

Selective control of synaptic plasticity in heterogeneous networks through transcranial alternating current stimulation (tACS)

Aref Pariz, Daniel Trotter, Axel Hutt, Jeremie Lefebvre

PLOS Computational Biology: published April 27, 2023 | https://doi.org/10.1371/journal.pcbi.1010736

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

PLOS Computational Biology: published April 27, 2023 | https://doi.org/10.1371/journal.pcbi.1010645

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

PLOS Computational Biology: published April 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011083

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

PLOS Computational Biology: published April 28, 2023 | https://doi.org/10.1371/journal.pcbi.1011086

Correction: Bayesian parameter estimation for dynamical models in systems biology

Nathaniel J. Linden, Boris Kramer, Padmini Rangamani

PLOS Computational Biology: published April 5, 2023 | https://doi.org/10.1371/journal.pcbi.1011041

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Correction: Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis

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PLOS Computational Biology: published April 14, 2023 | https://doi.org/10.1371/journal.pcbi.1011065

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Correction: Spatial and temporal correlations in human cortex are inherently linked and predicted by functional hierarchy, vigilance state as well as antiepileptic drug load

Paul Manuel Müller, Christian Meisel

PLOS Computational Biology: published April 27, 2023 | https://doi.org/10.1371/journal.pcbi.1011094

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