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June 2022

PCA visualization of LSTM hidden layer activity of an example 7-hidden-unit RNN while performing a 2-back working memory task. Visualized are the representations of different input stimuli (each represented with a different color) when in an unprioritized state in working memory. Solid gray arrow denotes the stimulus coding axis, which will rotate counterclockwise in the image plane (defined by the 1st and 2nd PCs) as the stimulus transitions to a prioritized state (indicated by the dashed gray arrow).

Image Credit: Quan Wan, Po'stl'ab, University of Wisconsin-Madison

Editorials

Advancing code sharing in the computational biology community

Lauren Cadwallader, Feilim Mac Gabhann, Jason Papin, Virginia E. Pitzer

Ten simple rules for succeeding as an underrepresented STEM undergraduate

Melanie Duc Bo Massey, Suchinta Arif, Shanukie Embuldeniya, Karma Nanglu, Joseph Bielawski

Ten simple rules for good research practice

Simon Schwab, Perrine Janiaud, Michael Dayan, Valentin Amrhein, Radoslaw Panczak, Patricia M. Palagi, Lars G. Hemkens, Meike Ramon, Nicolas Rothen, Stephen Senn, Eva Furrer, Leonhard Held

Education

Ten simple rules for managing communications with a large number of coauthors

Robert Muscarella, Lourens Poorter

Perspectives

Ten simple rules for good leadership

Philip E. Bourne

Ten simple rules for improving communication among scientists

Carla Bautista, Narjes Alfuraiji, Anna Drangowska-Way, Karishma Gangwani, Alida de Flamingh, Philip E. Bourne

Research Articles

Developmental shifts in computations used to detect environmental controllability

Hillary A. Raab, Careen Foord, Romain Ligneul, Catherine A. Hartley

Improved transcriptome assembly using a hybrid of long and short reads with StringTie

Alaina Shumate, Brandon Wong, Geo Pertea, Mihaela Pertea

Spatial modelling for population replacement of mosquito vectors at continental scale

Nicholas J. Beeton, Andrew Wilkins, Adrien Ickowicz, Keith R. Hayes, Geoffrey R. Hosack

Role of water-bridged interactions in metal ion coupled protein allostery

Xingyue Guan, Cheng Tan, Wenfei Li, Wei Wang, D. Thirumalai

sumSTAAR: A flexible framework for gene-based association studies using GWAS summary statistics

Nadezhda M. Belonogova, Gulnara R. Svishcheva, Anatoly V. Kirichenko, Irina V. Zorkoltseva, Yakov A. Tsepilov, Tatiana I. Axenovich

fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions

Natalia A. Szulc, Zuzanna Mackiewicz, Janusz M. Bujnicki, Filip Stefaniak

Priority-based transformations of stimulus representation in visual working memory

Quan Wan, Jorge A. Menendez, Bradley R. Postle

Pulmonary drug delivery and retention: A computational study to identify plausible parameters based on a coupled airway-mucus flow model

Aranyak Chakravarty, Mahesh V. Panchagnula, Alladi Mohan, Neelesh A. Patankar

Radical pairs may explain reactive oxygen species-mediated effects of hypomagnetic field on neurogenesis

Rishabh Rishabh, Hadi Zadeh-Haghighi, Dennis Salahub, Christoph Simon

Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies

Cosimo Lupo, Natanael Spisak, Aleksandra M. Walczak, Thierry Mora

scAmpi—A versatile pipeline for single-cell RNA-seq analysis from basics to clinics

Anne Bertolini, Michael Prummer, Mustafa Anil Tuncel, Ulrike Menzel, María Lourdes Rosano-González, Jack Kuipers, Daniel Johannes Stekhoven, Tumor Profiler consortium, Niko Beerenwinkel, Franziska Singer

CellDynaMo–stochastic reaction-diffusion-dynamics model: Application to search-and-capture process of mitotic spindle assembly

Evgenii Kliuchnikov, Artem Zhmurov, Kenneth A. Marx, Alex Mogilner, Valeri Barsegov

Addressing delayed case reporting in infectious disease forecast modeling

Lauren J. Beesley, Dave Osthus, Sara Y. Del Valle

From affinity selection to kinetic selection in Germinal Centre modelling

Danial Lashgari, Elena Merino Tejero, Michael Meyer-Hermann, Mathieu A. F. Claireaux, Marit J. van Gils, Huub C. J. Hoefsloot, Antoine H. C. van Kampen

A musculoskeletal finite element model of rat knee joint for evaluating cartilage biomechanics during gait

Gustavo A. Orozco, Kalle Karjalainen, Eng Kuan Moo, Lauri Stenroth, Petri Tanska, Jaqueline Lourdes Rios, Teemu V. Tuomainen, Mikko J. Nissi, Hanna Isaksson, Walter Herzog, Rami K. Korhonen

Strain design optimization using reinforcement learning

Maryam Sabzevari, Sandor Szedmak, Merja Penttilä, Paula Jouhten, Juho Rousu

Quantifying the impact of ecological memory on the dynamics of interacting communities

Moein Khalighi, Guilhem Sommeria-Klein, Didier Gonze, Karoline Faust, Leo Lahti

Induced fit with replica exchange improves protein complex structure prediction

Ameya Harmalkar, Sai Pooja Mahajan, Jeffrey J. Gray

Fluid mechanics of the zebrafish embryonic heart trabeculation

Adriana Gaia Cairelli, Renee Wei-Yan Chow, Julien Vermot, Choon Hwai Yap

Non-monotonic effects of GABAergic synaptic inputs on neuronal firing

Aghil Abed Zadeh, Brandon D. Turner, Nicole Calakos, Nicolas Brunel

Nanoscale organization of ryanodine receptor distribution and phosphorylation pattern determines the dynamics of calcium sparks

María Hernández Mesa, Jonas van den Brink, William E. Louch, Kimberly J. McCabe, Padmini Rangamani

Model-checking ecological state-transition graphs

Colin Thomas, Maximilien Cosme, Cédric Gaucherel, Franck Pommereau

Whole community invasions and the integration of novel ecosystems

Colin Campbell, Laura Russo, Réka Albert, Angus Buckling, Katriona Shea

Identification of upstream transcription factor binding sites in orthologous genes using mixed Student’s t-test statistics

Tinghua Huang, Hong Xiao, Qi Tian, Zhen He, Cheng Yuan, Zezhao Lin, Xuejun Gao, Min Yao

Data-dependent visualization of biological networks in the web-browser with NDExEdit

Florian Auer, Simone Mayer, Frank Kramer

Annotation-free delineation of prokaryotic homology groups

Yongze Yin, Huw A. Ogilvie, Luay Nakhleh

Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence

Fateme Pourhasanzade, Swami Iyer, Jesslyn Tjendra, Lotta Landor, Selina Våge

The lexical categorization model: A computational model of left ventral occipito-temporal cortex activation in visual word recognition

Benjamin Gagl, Fabio Richlan, Philipp Ludersdorfer, Jona Sassenhagen, Susanne Eisenhauer, Klara Gregorova, Christian J. Fiebach

Analysis of emergent patterns in crossing flows of pedestrians reveals an invariant of ‘stripe’ formation in human data

Pratik Mullick, Sylvain Fontaine, Cécile Appert-Rolland, Anne-Hélène Olivier, William H. Warren, Julien Pettré

SALARECON connects the Atlantic salmon genome to growth and feed efficiency

Maksim Zakhartsev, Filip Rotnes, Marie Gulla, Ove Øyås, Jesse C. J. van Dam, Maria Suarez-Diez, Fabian Grammes, Róbert Anton Hafþórsson, Wout van Helvoirt, Jasper J. Koehorst, Peter J. Schaap, Yang Jin, Liv Torunn Mydland, Arne B. Gjuvsland, Simen R. Sandve, Vitor A. P. Martins dos Santos, Jon Olav Vik

Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI)

Anika Liu, Namshik Han, Jordi Munoz-Muriedas, Andreas Bender

Design and execution of a verification, validation, and uncertainty quantification plan for a numerical model of left ventricular flow after LVAD implantation

Alfonso Santiago, Constantine Butakoff, Beatriz Eguzkitza, Richard A. Gray, Karen May-Newman, Pras Pathmanathan, Vi Vu, Mariano Vázquez

Differential methods for assessing sensitivity in biological models

Rachel Mester, Alfonso Landeros, Chris Rackauckas, Kenneth Lange

cytoNet: Spatiotemporal network analysis of cell communities

Arun S. Mahadevan, Byron L. Long, Chenyue W. Hu, David T. Ryan, Nicolas E. Grandel, George L. Britton, Marisol Bustos, Maria A. Gonzalez Porras, Katerina Stojkova, Andrew Ligeralde, Hyeonwi Son, John Shannonhouse, Jacob T. Robinson, Aryeh Warmflash, Eric M. Brey, Yu Shin Kim, Amina A. Qutub

Discrete modeling for integration and analysis of large-scale signaling networks

Pierre Vignet, Jean Coquet, Sébastien Auber, Matéo Boudet, Anne Siegel, Nathalie Théret

A mechanism for punctuating equilibria during mammalian vocal development

Thiago T. Varella, Yisi S. Zhang, Daniel Y. Takahashi, Asif A. Ghazanfar

Modeling cell biological features of meiotic chromosome pairing to study interlock resolution

Erik J. Navarro, Wallace F. Marshall, Jennifer C. Fung

Direct reciprocity between individuals that use different strategy spaces

Laura Schmid, Christian Hilbe, Krishnendu Chatterjee, Martin A. Nowak

Pre- and postsynaptically expressed spike-timing-dependent plasticity contribute differentially to neuronal learning

Beatriz Eymi Pimentel Mizusaki, Sally Si Ying Li, Rui Ponte Costa, Per Jesper Sjöström

Explainable detection of adverse drug reaction with imbalanced data distribution

Jin Wang, Liang-Chih Yu, Xuejie Zhang

SPF: A spatial and functional data analytic approach to cell imaging data

Thao Vu, Julia Wrobel, Benjamin G. Bitler, Erin L. Schenk, Kimberly R. Jordan, Debashis Ghosh

Orchestrated neuronal migration and cortical folding: A computational and experimental study

Shuolun Wang, Kengo Saito, Hiroshi Kawasaki, Maria A. Holland

Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach

Mahmudul Hasan Rifat, Jamil Ahmed, Milad Ahmed, Foeaz Ahmed, Airin Gulshan, Mahmudul Hasan

A weighted constraint satisfaction approach to human goal-directed decision making

Yuxuan Li, James L. McClelland

Active inference unifies intentional and conflict-resolution imperatives of motor control

Antonella Maselli, Pablo Lanillos, Giovanni Pezzulo

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

Shengbo Wang, David García-Seisdedos, Ananth Prakash, Deepti Jaiswal Kundu, Andrew Collins, Nancy George, Silvie Fexova, Pablo Moreno, Irene Papatheodorou, Andrew R. Jones, Juan Antonio Vizcaíno

Size regulation of multiple organelles competing for a limiting subunit pool

Deb Sankar Banerjee, Shiladitya Banerjee

Metastable spiking networks in the replica-mean-field limit

Luyan Yu, Thibaud O. Taillefumier

Efficient Bayesian inference for mechanistic modelling with high-throughput data

Simon Martina Perez, Heba Sailem, Ruth E. Baker

Neural circuit mechanisms of hierarchical sequence learning tested on large-scale recording data

Toshitake Asabuki, Prajakta Kokate, Tomoki Fukai

Combined computational modeling and experimental analysis integrating chemical and mechanical signals suggests possible mechanism of shoot meristem maintenance

Mikahl Banwarth-Kuhn, Kevin Rodriguez, Christian Michael, Calvin-Khang Ta, Alexander Plong, Eric Bourgain-Chang, Ali Nematbakhsh, Weitao Chen, Amit Roy-Chowdhury, G. Venugopala Reddy, Mark Alber

Error-based or target-based? A unified framework for learning in recurrent spiking networks

Cristiano Capone, Paolo Muratore, Pier Stanislao Paolucci

SCRaPL: A Bayesian hierarchical framework for detecting technical associates in single cell multiomics data

Christos Maniatis, Catalina A. Vallejos, Guido Sanguinetti

Sequence learning, prediction, and replay in networks of spiking neurons

Younes Bouhadjar, Markus Diesmann, Dirk J. Wouters, Tom Tetzlaff

A method for the inference of cytokine interaction networks

Joanneke E. Jansen, Dominik Aschenbrenner, Holm H. Uhlig, Mark C. Coles, Eamonn A. Gaffney

Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases

Christian Degnbol Madsen, Jotun Hein, Christopher T. Workman

Topological Sholl descriptors for neuronal clustering and classification

Reem Khalil, Sadok Kallel, Ahmad Farhat, Pawel Dlotko

Tracking the contribution of inductive bias to individualised internal models

Balázs Török, David G. Nagy, Mariann Kiss, Karolina Janacsek, Dezső Németh, Gergő Orbán

Epidemic management and control through risk-dependent individual contact interventions

Tapio Schneider, Oliver R. A. Dunbar, Jinlong Wu, Lucas Böttcher, Dmitry Burov, Alfredo Garbuno-Inigo, Gregory L. Wagner, Sen Pei, Chiara Daraio, Raffaele Ferrari, Jeffrey Shaman

Image-based parameter inference for epithelial mechanics

Goshi Ogita, Takefumi Kondo, Keisuke Ikawa, Tadashi Uemura, Shuji Ishihara, Kaoru Sugimura

Interpretable pairwise distillations for generative protein sequence models

Christoph Feinauer, Barthelemy Meynard-Piganeau, Carlo Lucibello

Modeling cortical synaptic effects of anesthesia and their cholinergic reversal

Bolaji P. Eniwaye, Victoria Booth, Anthony G. Hudetz, Michal Zochowski

LaDIVA: A neurocomputational model providing laryngeal motor control for speech acquisition and production

Hasini R. Weerathunge, Gabriel A. Alzamendi, Gabriel J. Cler, Frank H. Guenther, Cara E. Stepp, Matías Zañartu

Identifying control ensembles for information processing within the cortico-basal ganglia-thalamic circuit

Catalina Vich, Matthew Clapp, Jonathan E. Rubin, Timothy Verstynen

Evidence for influenza and RSV interaction from 10 years of enhanced surveillance in Nha Trang, Vietnam, a modelling study

Naomi R. Waterlow, Michiko Toizumi, Edwin van Leeuwen, Hien-Anh Thi Nguyen, Lay Myint-Yoshida, Rosalind M. Eggo, Stefan Flasche

MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments

Hamid Alinejad-Rokny, Rassa Ghavami Modegh, Hamid R. Rabiee, Ehsan Ramezani Sarbandi, Narges Rezaie, Kin Tung Tam, Alistair R. R. Forrest

Mathematical modeling of the microtubule detyrosination/tyrosination cycle for cell-based drug screening design

Jeremy Grignard, Véronique Lamamy, Eva Vermersch, Philippe Delagrange, Jean-Philippe Stephan, Thierry Dorval, François Fages

Data-based stochastic modeling reveals sources of activity bursts in single-cell TGF-β signaling

Niklas Kolbe, Lorenz Hexemer, Lukas-Malte Bammert, Alexander Loewer, Mária Lukáčová-Medvid’ová, Stefan Legewie

An ensemble forecast system for tracking dynamics of dengue outbreaks and its validation in China

Yuliang Chen, Tao Liu, Xiaolin Yu, Qinghui Zeng, Zixi Cai, Haisheng Wu, Qingying Zhang, Jianpeng Xiao, Wenjun Ma, Sen Pei, Pi Guo

Computational analysis of memory consolidation following inhibitory avoidance (IA) training in adult and infant rats: Critical roles of CaMKIIα and MeCP2

Yili Zhang, Paul Smolen, Cristina M. Alberini, Douglas A. Baxter, John H. Byrne

Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation

Raphael R. Eguchi, Christian A. Choe, Po-Ssu Huang

Covalent docking and molecular dynamics simulations reveal the specificity-shifting mutations Ala237Arg and Ala237Lys in TEM beta-lactamase

Gabriel Monteiro da Silva, Jordan Yang, Bunlong Leang, Jessie Huang, Daniel M. Weinreich, Brenda M. Rubenstein

Characterizing superspreading potential of infectious disease: Decomposition of individual transmissibility

Shi Zhao, Marc K. C. Chong, Sukhyun Ryu, Zihao Guo, Mu He, Boqiang Chen, Salihu S. Musa, Jingxuan Wang, Yushan Wu, Daihai He, Maggie H. Wang

The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility

Verónica S. Martínez, Pedro A. Saa, Jason Jooste, Kanupriya Tiwari, Lake-Ee Quek, Lars K. Nielsen

Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning

Alex X. Lu, Amy X. Lu, Iva Pritišanac, Taraneh Zarin, Julie D. Forman-Kay, Alan M. Moses

Corrections

Correction: A probabilistic model for the ultradian timing of REM sleep in mice

Sung-Ho Park, Justin Baik, Jiso Hong, Hanna Antila, Benjamin Kurland, Shinjae Chung, Franz Weber

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Correction: Stability of spontaneous, correlated activity in mouse auditory cortex

Richard F. Betzel, Katherine C. Wood, Christopher Angeloni, Maria Neimark Geffen, Danielle S. Bassett

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