February 2021

Unbiased quantitative phenotypic analysis of microscopy images of cells or organoids grown in 3D in large enough numbers to reach statistical clarity remains a fundamental challenge. Mergenthaler, Hariharan et al. report that using data driven voxel-based features and machine learning it is possible to analyze complex 3D image data without compressing them to 2D, identifying individual cells or using computationally intensive deep learning techniques. They provide the means for facile discovery and interpretation of meaningful patterns in a high dimensional feature space without complex image processing and prior knowledge or assumptions about the feature space.

Image Credit: Philipp Mergenthaler, Charité - Universitätsmedizin Berlin, Santosh Hariharan and David Andrews, Sunnybrook Research Institute, Toronto.

Editorials

Ten simple rules for engaging with artificial intelligence in biomedicine

Avni Malik, Paranjay Patel, Lubaina Ehsan, Shan Guleria, Thomas Hartka, Sodiq Adewole, Sana Syed

PLOS Computational Biology: published February 11, 2021 | https://doi.org/10.1371/journal.pcbi.1008531

Ten simple rules for navigating the computational aspect of an interdisciplinary PhD

Sabrina Islam, Christine A. Wells

PLOS Computational Biology: published February 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008554

Ten simple rules for running and managing virtual internships

Johannes Werner, Debora Jeske

PLOS Computational Biology: published February 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008599

Ten simple rules for starting (and sustaining) an academic data science initiative

Micaela S. Parker, Arlyn E. Burgess, Philip E. Bourne

PLOS Computational Biology: published February 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008628

Ten simple rules for getting started with command-line bioinformatics

Parice A. Brandies, Carolyn J. Hogg

PLOS Computational Biology: published February 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008645

Ten simple rules for writing compelling recommendation letters

Jennifer H. Kong, Latishya J. Steele, Crystal M. Botham

PLOS Computational Biology: published February 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008656

Ten simple rules for hosting artists in a scientific lab

Matthias C. Rillig, Karine Bonneval, Christian de Lutz, Johannes Lehmann, India Mansour, Regine Rapp, Saša Spačal, Vera Meyer

PLOS Computational Biology: published February 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008675

On the open-source landscape of PLOS Computational Biology

Mathieu Boudreau, Jean-Baptiste Poline, Pierre Bellec, Nikola Stikov

PLOS Computational Biology: published February 11, 2021 | https://doi.org/10.1371/journal.pcbi.1008725

Education Articles

Using prototyping to choose a bioinformatics workflow management system

Michael Jackson, Kostas Kavoussanakis, Edward W. J. Wallace

PLOS Computational Biology: published February 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008622

Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa

Verena Ras, Gerrit Botha, Shaun Aron, Katie Lennard, Imane Allali, Shantelle Claassen-Weitz, Kilaza Samson Mwaikono, Dane Kennedy, Jessica R. Holmes, Gloria Rendon, Sumir Panji, Christopher J Fields, Nicola Mulder

PLOS Computational Biology: published February 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008640

An integrated, modular approach to data science education in microbiology

Kimberly A. Dill-McFarland, Stephan G. König, Florent Mazel, David C. Oliver, Lisa M. McEwen, Kris Y. Hong, Steven J. Hallam

PLOS Computational Biology: published February 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008661

Perspective

Evaluating epidemic forecasts in an interval format

Johannes Bracher, Evan L. Ray, Tilmann Gneiting, Nicholas G. Reich

PLOS Computational Biology: published February 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008618

Research Articles

On the preservation of vessel bifurcations during flow-mediated angiogenic remodelling

Lowell T. Edgar, Claudio A. Franco, Holger Gerhardt, Miguel O. Bernabeu

PLOS Computational Biology: published February 4, 2021 | https://doi.org/10.1371/journal.pcbi.1007715

Efficient and flexible Integration of variant characteristics in rare variant association studies using integrated nested Laplace approximation

Hana Susak, Laura Serra-Saurina, German Demidov, Raquel Rabionet, Laura Domènech, Mattia Bosio, Francesc Muyas, Xavier Estivill, Geòrgia Escaramís, Stephan Ossowski

PLOS Computational Biology: published February 19, 2021 | https://doi.org/10.1371/journal.pcbi.1007784

Unsupervised manifold learning of collective behavior

Mathew Titus, George Hagstrom, James R. Watson

PLOS Computational Biology: published February 12, 2021 | https://doi.org/10.1371/journal.pcbi.1007811

A network model of the barrel cortex combined with a differentiator detector reproduces features of the behavioral response to single-neuron stimulation

Davide Bernardi, Guy Doron, Michael Brecht, Benjamin Lindner

PLOS Computational Biology: published February 8, 2021 | https://doi.org/10.1371/journal.pcbi.1007831

State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane

Marc A. Dämgen, Philip C. Biggin

PLOS Computational Biology: published February 11, 2021 | https://doi.org/10.1371/journal.pcbi.1007856

Ephaptic coupling in white matter fibre bundles modulates axonal transmission delays

Helmut Schmidt, Gerald Hahn, Gustavo Deco, Thomas R. Knösche

PLOS Computational Biology: published February 8, 2021 | https://doi.org/10.1371/journal.pcbi.1007858

Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees

George G. Vega Yon, Duncan C. Thomas, John Morrison, Huaiyu Mi, Paul D. Thomas, Paul Marjoram

PLOS Computational Biology: published February 18, 2021 | https://doi.org/10.1371/journal.pcbi.1007948

REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution

Casey A. Cole, Nourhan S. Daigham, Gaohua Liu, Gaetano T. Montelione, Homayoun Valafar

PLOS Computational Biology: published February 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008060

Neural surprise in somatosensory Bayesian learning

Sam Gijsen, Miro Grundei, Robert T. Lange, Dirk Ostwald, Felix Blankenburg

PLOS Computational Biology: published February 2, 2021 | https://doi.org/10.1371/journal.pcbi.1008068

Computational prediction of drug response in short QT syndrome type 1 based on measurements of compound effect in stem cell-derived cardiomyocytes

Karoline Horgmo Jæger, Samuel Wall, Aslak Tveito

PLOS Computational Biology: published February 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008089

Quantitative profiling of protease specificity

Boris I. Ratnikov, Piotr Cieplak, Albert G. Remacle, Elise Nguyen, Jeffrey W. Smith

PLOS Computational Biology: published February 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008101

Investigating the representation of uncertainty in neuronal circuits

Guillaume P. Dehaene, Ruben Coen-Cagli, Alexandre Pouget

PLOS Computational Biology: published February 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008138

Spectrally specific temporal analyses of spike-train responses to complex sounds: A unifying framework

Satyabrata Parida, Hari Bharadwaj, Michael G. Heinz

PLOS Computational Biology: published February 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008155

Role of neutrophil extracellular traps in regulation of lung cancer invasion and metastasis: Structural insights from a computational model

Junho Lee, Donggu Lee, Sean Lawler, Yangjin Kim

PLOS Computational Biology: published February 17, 2021 | https://doi.org/10.1371/journal.pcbi.1008257

A mesoscopic simulator to uncover heterogeneity and evolutionary dynamics in tumors

Juan Jiménez-Sánchez, Álvaro Martínez-Rubio, Anton Popov, Julián Pérez-Beteta, Youness Azimzade, David Molina-García, Juan Belmonte-Beitia, Gabriel F. Calvo, Víctor M. Pérez-García

PLOS Computational Biology: published February 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008266

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

Wei Lu, Carlos Bueno, Nicholas P. Schafer, Joshua Moller, Shikai Jin, Xun Chen, Mingchen Chen, Xinyu Gu, Aram Davtyan, Juan J. de Pablo, Peter G. Wolynes

PLOS Computational Biology: published February 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008308

AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses

Filip Stefaniak, Janusz M. Bujnicki

PLOS Computational Biology: published February 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008309

Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model

Jordan Douglas, Rong Zhang, Remco Bouckaert

PLOS Computational Biology: published February 2, 2021 | https://doi.org/10.1371/journal.pcbi.1008322

A model of developmental canalization, applied to human cranial form

Philipp Mitteroecker, Ekaterina Stansfield

PLOS Computational Biology: published February 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008381

Factors influencing estimates of HIV-1 infection timing using BEAST

Bethany Dearlove, Sodsai Tovanabutra, Christopher L. Owen, Eric Lewitus, Yifan Li, Eric Sanders-Buell, Meera Bose, Anne-Marie O’Sullivan, Gustavo Kijak, Shana Miller, Kultida Poltavee, Jenica Lee, Lydia Bonar, Elizabeth Harbolick, Bahar Ahani, Phuc Pham, Hannah Kibuuka, Lucas Maganga, Sorachai Nitayaphan, Fred K. Sawe, Jerome H. Kim, Leigh Anne Eller, Sandhya Vasan, Robert Gramzinski, Nelson L. Michael, Merlin L. Robb, Morgane Rolland, the RV217 Study Team

PLOS Computational Biology: published February 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008537

Functional parcellation of mouse visual cortex using statistical techniques reveals response-dependent clustering of cortical processing areas

Mari Ganesh Kumar, Ming Hu, Aadhirai Ramanujan, Mriganka Sur, Hema A. Murthy

PLOS Computational Biology: published February 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008548

Neural signatures of arbitration between Pavlovian and instrumental action selection

Samuel J. Gershman, Marc Guitart-Masip, James F. Cavanagh

PLOS Computational Biology: published February 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008553

End-to-end neural system identification with neural information flow

K. Seeliger, L. Ambrogioni, Y. Güçlütürk, L. M. van den Bulk, U. Güçlü, M. A. J. van Gerven

PLOS Computational Biology: published February 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008558

The role of children in the spread of COVID-19: Using household data from Bnei Brak, Israel, to estimate the relative susceptibility and infectivity of children

Itai Dattner, Yair Goldberg, Guy Katriel, Rami Yaari, Nurit Gal, Yoav Miron, Arnona Ziv, Rivka Sheffer, Yoram Hamo, Amit Huppert

PLOS Computational Biology: published February 11, 2021 | https://doi.org/10.1371/journal.pcbi.1008559

A mathematical model of the role of aggregation in sonic hedgehog signalling

Daniel J. A. Derrick, Kathryn Wolton, Richard A. Currie, Marcus John Tindall

PLOS Computational Biology: published February 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008562

Brain-inspired model for early vocal learning and correspondence matching using free-energy optimization

Alexandre Pitti, Mathias Quoy, Sofiane Boucenna, Catherine Lavandier

PLOS Computational Biology: published February 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008566

On the evolution and development of morphological complexity: A view from gene regulatory networks

Pascal F. Hagolani, Roland Zimm, Renske Vroomans, Isaac Salazar-Ciudad

PLOS Computational Biology: published February 24, 2021 | https://doi.org/10.1371/journal.pcbi.1008570

Deriving fine-scale models of human mobility from aggregated origin-destination flow data

Constanze Ciavarella, Neil M. Ferguson

PLOS Computational Biology: published February 11, 2021 | https://doi.org/10.1371/journal.pcbi.1008588

Relevance of intra-hospital patient movements for the spread of healthcare-associated infections within hospitals - a mathematical modeling study

Hannan Tahir, Luis Eduardo López-Cortés, Axel Kola, Dafna Yahav, André Karch, Hanjue Xia, Johannes Horn, Konrad Sakowski, Monika J. Piotrowska, Leonard Leibovici, Rafael T. Mikolajczyk, Mirjam E. Kretzschmar

PLOS Computational Biology: published February 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008600

Directed attenuation to enhance vaccine immunity

Rustom Antia, Hasan Ahmed, James J. Bull

PLOS Computational Biology: published February 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008602

Localization, epidemic transitions, and unpredictability of multistrain epidemics with an underlying genotype network

Blake J. M. Williams, Guillaume St-Onge, Laurent Hébert-Dufresne

PLOS Computational Biology: published February 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008606

miRNA normalization enables joint analysis of several datasets to increase sensitivity and to reveal novel miRNAs differentially expressed in breast cancer

Shay Ben-Elazar, Miriam Ragle Aure, Kristin Jonsdottir, Suvi-Katri Leivonen, Vessela N. Kristensen, Emiel A. M. Janssen, Kristine Kleivi Sahlberg, Ole Christian Lingjærde, Zohar Yakhini

PLOS Computational Biology: published February 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008608

Neural manifold under plasticity in a goal driven learning behaviour

Barbara Feulner, Claudia Clopath

PLOS Computational Biology: published February 5, 2021 | https://doi.org/10.1371/journal.pcbi.1008621

Rapid 3D phenotypic analysis of neurons and organoids using data-driven cell segmentation-free machine learning

Philipp Mergenthaler, Santosh Hariharan, James M. Pemberton, Corey Lourenco, Linda Z. Penn, David W. Andrews

PLOS Computational Biology: published February 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008630

Modeling drug response using network-based personalized treatment prediction (NetPTP) with applications to inflammatory bowel disease

Lichy Han, Zahra N. Sayyid, Russ B. Altman

PLOS Computational Biology: published February 5, 2021 | https://doi.org/10.1371/journal.pcbi.1008631

Building clone-consistent ecosystem models

Gerrit Ansmann, Tobias Bollenbach

PLOS Computational Biology: published February 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008635

A numerical framework for mechano-regulated tendon healing—Simulation of early regeneration of the Achilles tendon

Thomas Notermans, Petri Tanska, Rami K. Korhonen, Hanifeh Khayyeri, Hanna Isaksson

PLOS Computational Biology: published February 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008636

Ancestral haplotype reconstruction in endogamous populations using identity-by-descent

Kelly Finke, Michael Kourakos, Gabriela Brown, Huyen Trang Dang, Shi Jie Samuel Tan, Yuval B. Simons, Shweta Ramdas, Alejandro A. Schäffer, Rachel L. Kember, Maja Bućan, Sara Mathieson

PLOS Computational Biology: published February 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008638

Adaptive social contact rates induce complex dynamics during epidemics

Ronan F. Arthur, James H. Jones, Matthew H. Bonds, Yoav Ram, Marcus W. Feldman

PLOS Computational Biology: published February 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008639

Independent component analysis recovers consistent regulatory signals from disparate datasets

Anand V. Sastry, Alyssa Hu, David Heckmann, Saugat Poudel, Erol Kavvas, Bernhard O. Palsson

PLOS Computational Biology: published February 2, 2021 | https://doi.org/10.1371/journal.pcbi.1008647

Unraveling ChR2-driven stochastic Ca²⁺ dynamics in astrocytes: A call for new interventional paradigms

Arash Moshkforoush, Lakshmini Balachandar, Carolina Moncion, Karla A. Montejo, Jorge Riera

PLOS Computational Biology: published February 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008648

TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations

Qiao Liu, Lei Xie

PLOS Computational Biology: published February 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008653

Design principles for the glycoprotein quality control pathway

Aidan I. Brown, Elena F. Koslover

PLOS Computational Biology: published February 1, 2021 | https://doi.org/10.1371/journal.pcbi.1008654

When to wake up? The optimal waking-up strategies for starvation-induced persistence

Yusuke Himeoka, Namiko Mitarai

PLOS Computational Biology: published February 11, 2021 | https://doi.org/10.1371/journal.pcbi.1008655

Inferring the structures of signaling motifs from paired dynamic traces of single cells

Raymond A. Haggerty, Jeremy E. Purvis

PLOS Computational Biology: published February 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008657

Estimating the extrinsic incubation period of malaria using a mechanistic model of sporogony

Isaac J. Stopard, Thomas S. Churcher, Ben Lambert

PLOS Computational Biology: published February 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008658

Reproduction of patterns in melanocytic proliferations by agent-based simulation and geometric modeling

Günter Schneckenreither, Philipp Tschandl, Claire Rippinger, Christoph Sinz, Dominik Brunmeir, Nikolas Popper, Harald Kittler

PLOS Computational Biology: published February 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008660

Modulation of the dynamics of cerebellar Purkinje cells through the interaction of excitatory and inhibitory feedforward pathways

Yuanhong Tang, Lingling An, Ye Yuan, Qingqi Pei, Quan Wang, Jian K. Liu

PLOS Computational Biology: published February 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008670

Finding branched pathways in metabolic network via atom group tracking

Yiran Huang, Yusi Xie, Cheng Zhong, Fengfeng Zhou

PLOS Computational Biology: published February 2, 2021 | https://doi.org/10.1371/journal.pcbi.1008676

A comprehensive computational model of animal biosonar signal processing

Chen Ming, Stephanie Haro, Andrea Megela Simmons, James A. Simmons

PLOS Computational Biology: published February 17, 2021 | https://doi.org/10.1371/journal.pcbi.1008677

Dynamics of chromosomal target search by a membrane-integrated one-component receptor

Linda Martini, Sophie Brameyer, Elisabeth Hoyer, Kirsten Jung, Ulrich Gerland

PLOS Computational Biology: published February 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008680

KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions

Bingjie Xue, Benjamin Jordan, Saqib Rizvi, Kristen M. Naegle

PLOS Computational Biology: published February 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008681

Arrhythmogenic effects of ultra-long and bistable cardiac action potentials

Stewart Heitmann, Anton Shpak, Jamie I. Vandenberg, Adam P. Hill

PLOS Computational Biology: published February 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008683

Dynamics of COVID-19 under social distancing measures are driven by transmission network structure

Anjalika Nande, Ben Adlam, Justin Sheen, Michael Z. Levy, Alison L. Hill

PLOS Computational Biology: published February 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008684

ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways

Agatha Treveil, Balazs Bohar, Padhmanand Sudhakar, Lejla Gul, Luca Csabai, Marton Olbei, Martina Poletti, Matthew Madgwick, Tahila Andrighetti, Isabelle Hautefort, Dezso Modos, Tamas Korcsmaros

PLOS Computational Biology: published February 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008685

SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19

Giulia Fiscon, Federica Conte, Lorenzo Farina, Paola Paci

PLOS Computational Biology: published February 5, 2021 | https://doi.org/10.1371/journal.pcbi.1008686

Data-driven method to infer the seizure propagation patterns in an epileptic brain from intracranial electroencephalography

Viktor Sip, Meysam Hashemi, Anirudh N. Vattikonda, Marmaduke M. Woodman, Huifang Wang, Julia Scholly, Samuel Medina Villalon, Maxime Guye, Fabrice Bartolomei, Viktor K. Jirsa

PLOS Computational Biology: published February 17, 2021 | https://doi.org/10.1371/journal.pcbi.1008689

Fixation probabilities in graph-structured populations under weak selection

Benjamin Allen, Christine Sample, Patricia Steinhagen, Julia Shapiro, Matthew King, Timothy Hedspeth, Megan Goncalves

PLOS Computational Biology: published February 2, 2021 | https://doi.org/10.1371/journal.pcbi.1008695

Predicting therapeutic drugs for hepatocellular carcinoma based on tissue-specific pathways

Liang Yu, Meng Wang, Yang Yang, Fengdan Xu, Xu Zhang, Fei Xie, Lin Gao, Xiangzhi Li

PLOS Computational Biology: published February 9, 2021 | https://doi.org/10.1371/journal.pcbi.1008696

FastTrack: An open-source software for tracking varying numbers of deformable objects

Benjamin Gallois, Raphaël Candelier

PLOS Computational Biology: published February 11, 2021 | https://doi.org/10.1371/journal.pcbi.1008697

Sensing ecosystem dynamics via audio source separation: A case study of marine soundscapes off northeastern Taiwan

Tzu-Hao Lin, Tomonari Akamatsu, Yu Tsao

PLOS Computational Biology: published February 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008698

Tumor hepatitis B virus RNA identifies a clinically and molecularly distinct subset of hepatocellular carcinoma

Huat Chye Lim, John D. Gordan

PLOS Computational Biology: published February 9, 2021 | https://doi.org/10.1371/journal.pcbi.1008699

Learning poly-synaptic paths with traveling waves

Yoshiki Ito, Taro Toyoizumi

PLOS Computational Biology: published February 9, 2021 | https://doi.org/10.1371/journal.pcbi.1008700

Signatures of neutral evolution in exponentially growing tumors: A theoretical perspective

Hwai-Ray Tung, Rick Durrett

PLOS Computational Biology: published February 11, 2021 | https://doi.org/10.1371/journal.pcbi.1008701

The impact of phenotypic heterogeneity of tumour cells on treatment and relapse dynamics

Michael Raatz, Saumil Shah, Guranda Chitadze, Monika Brüggemann, Arne Traulsen

PLOS Computational Biology: published February 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008702

Freedom to choose between public resources promotes cooperation

Mohammad Salahshour

PLOS Computational Biology: published February 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008703

Mapping parameter spaces of biological switches

Rocky Diegmiller, Lun Zhang, Marcio Gameiro, Justinn Barr, Jasmin Imran Alsous, Paul Schedl, Stanislav Y. Shvartsman, Konstantin Mischaikow

PLOS Computational Biology: published February 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008711

Protective impacts of household-based tuberculosis contact tracing are robust across endemic incidence levels and community contact patterns

Joshua Havumaki, Ted Cohen, Chengwei Zhai, Joel C. Miller, Seth D. Guikema, Marisa C. Eisenberg, Jon Zelner

PLOS Computational Biology: published February 8, 2021 | https://doi.org/10.1371/journal.pcbi.1008713

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)

Renaud Van Damme, Martin Hölzer, Adrian Viehweger, Bettina Müller, Erik Bongcam-Rudloff, Christian Brandt

PLOS Computational Biology: published February 9, 2021 | https://doi.org/10.1371/journal.pcbi.1008716

Impact of between-tissue differences on pan-cancer predictions of drug sensitivity

John P. Lloyd, Matthew B. Soellner, Sofia D. Merajver, Jun Z. Li

PLOS Computational Biology: published February 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008720

Integrated information structure collapses with anesthetic loss of conscious arousal in Drosophila melanogaster

Angus Leung, Dror Cohen, Bruno van Swinderen, Naotsugu Tsuchiya

PLOS Computational Biology: published February 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008722

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships

Florian Huber, Lars Ridder, Stefan Verhoeven, Jurriaan H. Spaaks, Faruk Diblen, Simon Rogers, Justin J. J. van der Hooft

PLOS Computational Biology: published February 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008724

Balrog: A universal protein model for prokaryotic gene prediction

Markus J. Sommer, Steven L. Salzberg

PLOS Computational Biology: published February 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008727

Estimating the cumulative incidence of SARS-CoV-2 with imperfect serological tests: Exploiting cutoff-free approaches

Judith A. Bouman, Julien Riou, Sebastian Bonhoeffer, Roland R. Regoes

PLOS Computational Biology: published February 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008728

An antigenic diversification threshold for falciparum malaria transmission at high endemicity

Qixin He, Mercedes Pascual

PLOS Computational Biology: published February 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008729

DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks

Pablo Rodríguez-Mier, Nathalie Poupin, Carlo de Blasio, Laurent Le Cam, Fabien Jourdan

PLOS Computational Biology: published February 11, 2021 | https://doi.org/10.1371/journal.pcbi.1008730

Evidence for spreading seizure as a cause of theta-alpha activity electrographic pattern in stereo-EEG seizure recordings

Viktor Sip, Julia Scholly, Maxime Guye, Fabrice Bartolomei, Viktor Jirsa

PLOS Computational Biology: published February 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008731

Computational modeling of the gut microbiota reveals putative metabolic mechanisms of recurrent Clostridioides difficile infection

Michael A. Henson

PLOS Computational Biology: published February 22, 2021 | https://doi.org/10.1371/journal.pcbi.1008782

Cover

Data-driven phenotypic machine learning analysis for 3D microscopy

Editorials

Education Articles

Perspective

Related Articles

Research Articles

Related Articles

Related Articles

Corrections

Related Articles

Related Articles

Related Articles