Ten simple rules for building an enthusiastic iGEM team

Luis Garcia Morales, Niek H. A. Savelkoul, Zoë Robaey, Nico J. Claassens, Raymond H. J. Staals, Robert W. Smith

PLOS Computational Biology: published March 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009916

Ten simple rules for making a software tool workflow-ready

Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R. Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn Grüning, Ignacio Eguinoa, Philip Ewels, Carole Goble

PLOS Computational Biology: published March 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009823

Ten quick tips for deep learning in biology

Benjamin D. Lee, Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, Alexander J. Titus, Michael D. Kessler, Alexandra J. Lee, Marc G. Chevrette, Paul Allen Stewart, Thiago Britto-Borges, Evan M. Cofer, Kun-Hsing Yu, Juan Jose Carmona, Elana J. Fertig, Alexandr A. Kalinin, Brandon Signal, Benjamin J. Lengerich, Timothy J. Triche Jr., Simina M. Boca

PLOS Computational Biology: published March 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009803

Ten simple rules for finding and selecting R packages

Caroline J. Wendt, G. Brooke Anderson

PLOS Computational Biology: published March 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009884

Ten simple rules for principled simulation modelling

Laurel Fogarty, Madeleine Ammar, Thomas Holding, Adam Powell, Anne Kandler

PLOS Computational Biology: published March 31, 2022 | https://doi.org/10.1371/journal.pcbi.1009917

Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics

Erich Hellemann, Jennifer L. Walker, Mitchell A. Lesko, Dakshayini G. Chandrashekarappa, Martin C. Schmidt, Allyson F. O’Donnell, Jacob D. Durrant

PLOS Computational Biology: published March 2, 2022 | https://doi.org/10.1371/journal.pcbi.1009929

Missense variants in human ACE2 strongly affect binding to SARS-CoV-2 Spike providing a mechanism for ACE2 mediated genetic risk in Covid-19: A case study in affinity predictions of interface variants

Stuart A. MacGowan, Michael I. Barton, Mikhail Kutuzov, Omer Dushek, P. Anton van der Merwe, Geoffrey J. Barton

PLOS Computational Biology: published March 2, 2022 | https://doi.org/10.1371/journal.pcbi.1009922

Tumor immune cell clustering and its association with survival in African American women with ovarian cancer

Christopher Wilson, Alex C. Soupir, Ram Thapa, Jordan Creed, Jonathan Nguyen, Carlos Moran Segura, Travis Gerke, Joellen M. Schildkraut, Lauren C. Peres, Brooke L. Fridley

PLOS Computational Biology: published March 2, 2022 | https://doi.org/10.1371/journal.pcbi.1009900

The impact of individual perceptual and cognitive factors on collective states in a data-driven fish school model

Weijia Wang, Ramón Escobedo, Stéphane Sanchez, Clément Sire, Zhangang Han, Guy Theraulaz

PLOS Computational Biology: published March 2, 2022 | https://doi.org/10.1371/journal.pcbi.1009437

Estimates of the basic reproduction number for rubella using seroprevalence data and indicator-based approaches

Timos Papadopoulos, Emilia Vynnycky

PLOS Computational Biology: published March 3, 2022 | https://doi.org/10.1371/journal.pcbi.1008858

How does a small molecule bind at a cryptic binding site?

Yibing Shan, Venkatesh P. Mysore, Abba E. Leffler, Eric T. Kim, Shiori Sagawa, David E. Shaw

PLOS Computational Biology: published March 3, 2022 | https://doi.org/10.1371/journal.pcbi.1009817

Encoding time in neural dynamic regimes with distinct computational tradeoffs

Shanglin Zhou, Sotiris C. Masmanidis, Dean V. Buonomano

PLOS Computational Biology: published March 3, 2022 | https://doi.org/10.1371/journal.pcbi.1009271

Human discrimination and modeling of high-frequency complex tones shed light on the neural codes for pitch

Daniel R. Guest, Andrew J. Oxenham

PLOS Computational Biology: published March 3, 2022 | https://doi.org/10.1371/journal.pcbi.1009889

Autocrine signaling can explain the emergence of Allee effects in cancer cell populations

Philip Gerlee, Philipp M. Altrock, Adam Malik, Cecilia Krona, Sven Nelander

PLOS Computational Biology: published March 3, 2022 | https://doi.org/10.1371/journal.pcbi.1009844

Stimulating at the right time to recover network states in a model of the cortico-basal ganglia-thalamic circuit

Timothy O. West, Peter J. Magill, Andrew Sharott, Vladimir Litvak, Simon F. Farmer, Hayriye Cagnan

PLOS Computational Biology: published March 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009887

Global dynamics of microbial communities emerge from local interaction rules

Simon van Vliet, Christoph Hauert, Kyle Fridberg, Martin Ackermann, Alma Dal Co

PLOS Computational Biology: published March 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009877

Multiphysics and multiscale modeling of microthrombosis in COVID-19

He Li, Yixiang Deng, Zhen Li, Ander Dorken Gallastegi, Christos S. Mantzoros, Galit H. Frydman, George E. Karniadakis

PLOS Computational Biology: published March 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009892

Model-based identification of conditionally-essential genes from transposon-insertion sequencing data

Vishal Sarsani, Berent Aldikacti, Shai He, Rilee Zeinert, Peter Chien, Patrick Flaherty

PLOS Computational Biology: published March 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009273

Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition

Shin-ichi Koda, Shinji Saito

PLOS Computational Biology: published March 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009243

Bayesian calibration, process modeling and uncertainty quantification in biotechnology

Laura Marie Helleckes, Michael Osthege, Wolfgang Wiechert, Eric von Lieres, Marco Oldiges

PLOS Computational Biology: published March 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009223

Constructing benchmark test sets for biological sequence analysis using independent set algorithms

Samantha Petti, Sean R. Eddy

PLOS Computational Biology: published March 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009492

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PLOS Computational Biology: published March 8, 2022 | https://doi.org/10.1371/journal.pcbi.1009925

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Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart

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PLOS Computational Biology: published March 8, 2022 | https://doi.org/10.1371/journal.pcbi.1009947

The impact of the spatial heterogeneity of resistant cells and fibroblasts on treatment response

Masud M A, Jae-Young Kim, Cheol-Ho Pan, Eunjung Kim

PLOS Computational Biology: published March 9, 2022 | https://doi.org/10.1371/journal.pcbi.1009919

Bayesian inference of ancestral recombination graphs

Ali Mahmoudi, Jere Koskela, Jerome Kelleher, Yao-ban Chan, David Balding

PLOS Computational Biology: published March 9, 2022 | https://doi.org/10.1371/journal.pcbi.1009960

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Kaumadi Wijesooriya, Sameer A. Jadaan, Kaushalya L. Perera, Tanuveer Kaur, Mark Ziemann

PLOS Computational Biology: published March 9, 2022 | https://doi.org/10.1371/journal.pcbi.1009935

Base-resolution prediction of transcription factor binding signals by a deep learning framework

Qinhu Zhang, Ying He, Siguo Wang, Zhanheng Chen, Zhenhao Guo, Zhen Cui, Qi Liu, De-Shuang Huang

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Thalamic bursts modulate cortical synchrony locally to switch between states of global functional connectivity in a cognitive task

Oscar Portoles, Manuel Blesa, Marieke van Vugt, Ming Cao, Jelmer P. Borst

PLOS Computational Biology: published March 9, 2022 | https://doi.org/10.1371/journal.pcbi.1009407

Tumor cell intrinsic and extrinsic features predict prognosis in estrogen receptor positive breast cancer

Kevin Yao, Evelien Schaafsma, Baoyi Zhang, Chao Cheng

PLOS Computational Biology: published March 9, 2022 | https://doi.org/10.1371/journal.pcbi.1009495

A copula based topology preserving graph convolution network for clustering of single-cell RNA-seq data

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PLOS Computational Biology: published March 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009600

Personalized pathology test for Cardio-vascular disease: Approximate Bayesian computation with discriminative summary statistics learning

Ritabrata Dutta, Karim Zouaoui Boudjeltia, Christos Kotsalos, Alexandre Rousseau, Daniel Ribeiro de Sousa, Jean-Marc Desmet, Alain Van Meerhaeghe, Antonietta Mira, Bastien Chopard

PLOS Computational Biology: published March 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009910

The ability to classify patients based on gene-expression data varies by algorithm and performance metric

Stephen R. Piccolo, Avery Mecham, Nathan P. Golightly, Jérémie L. Johnson, Dustin B. Miller

PLOS Computational Biology: published March 11, 2022 | https://doi.org/10.1371/journal.pcbi.1009926

Characterization of intrinsically disordered regions in proteins informed by human genetic diversity

Shehab S. Ahmed, Zaara T. Rifat, Ruchi Lohia, Arthur J. Campbell, A. Keith Dunker, M. Sohel Rahman, Sumaiya Iqbal

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Estimating genetic variance contributed by a quantitative trait locus: A random model approach

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PLOS Computational Biology: published March 11, 2022 | https://doi.org/10.1371/journal.pcbi.1009923

Deep inference of seabird dives from GPS-only records: Performance and generalization properties

Amédée Roy, Sophie Lanco Bertrand, Ronan Fablet

PLOS Computational Biology: published March 11, 2022 | https://doi.org/10.1371/journal.pcbi.1009890

Automatic wound detection and size estimation using deep learning algorithms

Héctor Carrión, Mohammad Jafari, Michelle Dawn Bagood, Hsin-ya Yang, Roslyn Rivkah Isseroff, Marcella Gomez

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Motor-related signals support localization invariance for stable visual perception

Andrea Benucci

PLOS Computational Biology: published March 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009928

A network-based approach to integrate nutrient microenvironment in the prediction of synthetic lethality in cancer metabolism

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Evolution of innate behavioral strategies through competitive population dynamics

Tong Liang, Braden A. W. Brinkman

PLOS Computational Biology: published March 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009934

SMetABF: A rapid algorithm for Bayesian GWAS meta-analysis with a large number of studies included

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Does plasmid-based beta-lactam resistance increase E. coli infections: Modelling addition and replacement mechanisms

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The role of cell geometry and cell-cell communication in gradient sensing

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Deep learning tools and modeling to estimate the temporal expression of cell cycle proteins from 2D still images

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Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images

Romain Amyot, Arin Marchesi, Clemens M. Franz, Ignacio Casuso, Holger Flechsig

PLOS Computational Biology: published March 16, 2022 | https://doi.org/10.1371/journal.pcbi.1009970

Investigating key cell types and molecules dynamics in PyMT mice model of breast cancer through a mathematical model

Navid Mohammad Mirzaei, Navid Changizi, Alireza Asadpoure, Sumeyye Su, Dilruba Sofia, Zuzana Tatarova, Ioannis K. Zervantonakis, Young Hwan Chang, Leili Shahriyari

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RosettaSurf—A surface-centric computational design approach

Andreas Scheck, Stéphane Rosset, Michaël Defferrard, Andreas Loukas, Jaume Bonet, Pierre Vandergheynst, Bruno E. Correia

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SavvyCNV: Genome-wide CNV calling from off-target reads

Thomas W. Laver, Elisa De Franco, Matthew B. Johnson, Kashyap A. Patel, Sian Ellard, Michael N. Weedon, Sarah E. Flanagan, Matthew N. Wakeling

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Avalanches during epithelial tissue growth; Uniform Growth and a drosophila eye disc model

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Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species

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Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level

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In vitro machine learning-based CAR T immunological synapse quality measurements correlate with patient clinical outcomes

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Mathematical analysis of robustness of oscillations in models of the mammalian circadian clock

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Determining clinically relevant features in cytometry data using persistent homology

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Detection of focal source and arrhythmogenic substrate from body surface potentials to guide atrial fibrillation ablation

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Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins

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Chemotherapy-induced cachexia and model-informed dosing to preserve lean mass in cancer treatment

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Incorporating regulatory interactions into gene-set analyses for GWAS data: A controlled analysis with the MAGMA tool

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COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions

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Interactions between sensory prediction error and task error during implicit motor learning

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Dissecting mutational allosteric effects in alkaline phosphatases associated with different Hypophosphatasia phenotypes: An integrative computational investigation

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Transcriptome diversity is a systematic source of variation in RNA-sequencing data

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Cortical oscillations support sampling-based computations in spiking neural networks

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Isotope-assisted metabolic flux analysis as an equality-constrained nonlinear program for improved scalability and robustness

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Mining folded proteomes in the era of accurate structure prediction

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Biological action at a distance: Correlated pattern formation in adjacent tessellation domains without communication

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How the storage effect and the number of temporal niches affect biodiversity in stochastic and seasonal environments

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Pooled testing of traced contacts under superspreading dynamics

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Survival analysis of pathway activity as a prognostic determinant in breast cancer

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PLUS: Predicting cancer metastasis potential based on positive and unlabeled learning

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PLOS Computational Biology: published March 29, 2022 | https://doi.org/10.1371/journal.pcbi.1009956

Performance of early warning signals for disease re-emergence: A case study on COVID-19 data

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Inferring age-specific differences in susceptibility to and infectiousness upon SARS-CoV-2 infection based on Belgian social contact data

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Analysis of localized cAMP perturbations within a tissue reveal the effects of a local, dynamic gap junction state on ERK signaling

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PLOS Computational Biology: published March 30, 2022 | https://doi.org/10.1371/journal.pcbi.1009873

Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins

Lei Wang, Jiangguo Zhang, Dali Wang, Chen Song

PLOS Computational Biology: published March 30, 2022 | https://doi.org/10.1371/journal.pcbi.1009972

Addressing the mean-correlation relationship in co-expression analysis

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Pulsatile contractions and pattern formation in excitable actomyosin cortex

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SPOROS: A pipeline to analyze DISE/6mer seed toxicity

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Quantification of long-term doxorubicin response dynamics in breast cancer cell lines to direct treatment schedules

Grant R. Howard, Tyler A. Jost, Thomas E. Yankeelov, Amy Brock

PLOS Computational Biology: published March 31, 2022 | https://doi.org/10.1371/journal.pcbi.1009104

Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data

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Correction: Bayesian regression explains how human participants handle parameter uncertainty

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