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Table of Contents

January 2021

The DNA binding domain of protein p53 is found complexed with many other proteins and DNA in the Protein Data Bank (PDB). The outer wheel shows soft disordered (in orange) and interface (in blue) regions observed in alternative crystals of these complexes. In the center, we show that once mapped on the structure, the union of all soft disordered regions and the union of all the interface regions tend to involve the same amino acids in the protein.

Image Credit: Beatriz Seoane

Editorial

Ten simple rules for tackling your first mathematical models: A guide for graduate students by graduate students

Korryn Bodner, Chris Brimacombe, Emily S. Chenery, Ariel Greiner, Anne M. McLeod, Stephanie R. Penk, Juan S. Vargas Soto

Topic Page

Chemical graph generators

Mehmet Aziz Yirik, Christoph Steinbeck

Research Articles

Improving probabilistic infectious disease forecasting through coherence

Graham Casey Gibson, Kelly R. Moran, Nicholas G. Reich, Dave Osthus

Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions

Claudio Tomi-Andrino, Rupert Norman, Thomas Millat, Philippe Soucaille, Klaus Winzer, David A. Barrett, John King, Dong-Hyun Kim

Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility

Pedro Manuel Martínez-García, Miguel García-Torres, Federico Divina, José Terrón-Bautista, Irene Delgado-Sainz, Francisco Gómez-Vela, Felipe Cortés-Ledesma

Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers

Jonas Béal, Lorenzo Pantolini, Vincent Noël, Emmanuel Barillot, Laurence Calzone

Persistent thermal input controls steering behavior in Caenorhabditis elegans

Muneki Ikeda, Hirotaka Matsumoto, Eduardo J. Izquierdo

Coordinating cell polarization and morphogenesis through mechanical feedback

Samhita P. Banavar, Michael Trogdon, Brian Drawert, Tau-Mu Yi, Linda R. Petzold, Otger Campàs

Physical constraints on early blastomere packings

James Giammona, Otger Campàs

A multiscale model of complex endothelial cell dynamics in early angiogenesis

Daria Stepanova, Helen M. Byrne, Philip K. Maini, Tomás Alarcón

A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response

Evanthia Koukouli, Dennis Wang, Frank Dondelinger, Juhyun Park

HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data

Sára Sáray, Christian A. Rössert, Shailesh Appukuttan, Rosanna Migliore, Paola Vitale, Carmen A. Lupascu, Luca L. Bologna, Werner Van Geit, Armando Romani, Andrew P. Davison, Eilif Muller, Tamás F. Freund, Szabolcs Káli

Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology

Hamed Khakzad, Lotta Happonen, Yasaman Karami, Sounak Chowdhury, Gizem Ertürk Bergdahl, Michael Nilges, Guy Tran Van Nhieu, Johan Malmström, Lars Malmström

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

Zachary B. Haiman, Daniel C. Zielinski, Yuko Koike, James T. Yurkovich, Bernhard O. Palsson

Friendly-rivalry solution to the iterated n-person public-goods game

Yohsuke Murase, Seung Ki Baek

Causal network inference from gene transcriptional time-series response to glucocorticoids

Jonathan Lu, Bianca Dumitrascu, Ian C. McDowell, Brian Jo, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Timothy E. Reddy, Barbara E. Engelhardt

Dynamic bistable switches enhance robustness and accuracy of cell cycle transitions

Jan Rombouts, Lendert Gelens

Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants

Adil Alsiyabi, Ariadna Gonzalez Solis, Edgar B. Cahoon, Rajib Saha

Active probing to highlight approaching transitions to ictal states in coupled neural mass models

Vinícius Rezende Carvalho, Márcio Flávio Dutra Moraes, Sydney S. Cash, Eduardo Mazoni Andrade Marçal Mendes

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine

Linda K. Sundermann, Jeff Wintersinger, Gunnar Rätsch, Jens Stoye, Quaid Morris

Modelling thalamocortical circuitry shows that visually induced LTP changes laminar connectivity in human visual cortex

Rachael L. Sumner, Meg J. Spriggs, Alexander D. Shaw

Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission

David W. Eyre, Mirjam Laager, A. Sarah Walker, Ben S. Cooper, Daniel J. Wilson, on behalf of the CDC Modeling Infectious Diseases in Healthcare Program (MInD-Healthcare)

Identifying the drivers of multidrug-resistant Klebsiella pneumoniae at a European level

Viacheslav N. Kachalov, Huyen Nguyen, Suraj Balakrishna, Luisa Salazar-Vizcaya, Rami Sommerstein, Stefan P. Kuster, Anthony Hauser, Pia Abel zur Wiesch, Eili Klein, Roger D. Kouyos

The value of decreasing the duration of the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection

Bruce Y. Lee, Sarah M. Bartsch, Marie C. Ferguson, Patrick T. Wedlock, Kelly J. O’Shea, Sheryl S. Siegmund, Sarah N. Cox, James A. McKinnell

Computational modeling suggests binding-induced expansion of Epsin disordered regions upon association with AP2

N. Suhas Jagannathan, Christopher W. V. Hogue, Lisa Tucker-Kellogg

Breast cancer is marked by specific, Public T-cell receptor CDR3 regions shared by mice and humans

Miri Gordin, Hagit Philip, Alona Zilberberg, Moriah Gidoni, Raanan Margalit, Christopher Clouser, Kristofor Adams, Francois Vigneault, Irun R. Cohen, Gur Yaari, Sol Efroni

MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome

Preecha Patumcharoenpol, Massalin Nakphaichit, Gianni Panagiotou, Anchalee Senavonge, Narissara Suratannon, Wanwipa Vongsangnak

Contrasting mechanisms for hidden hearing loss: Synaptopathy vs myelin defects

Maral Budak, Karl Grosh, Aritra Sasmal, Gabriel Corfas, Michal Zochowski, Victoria Booth

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Network propagation of rare variants in Alzheimer’s disease reveals tissue-specific hub genes and communities

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Sensor-based localization of epidemic sources on human mobility networks

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The complexity of protein interactions unravelled from structural disorder

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The risks of using the chi-square periodogram to estimate the period of biological rhythms

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Rosetta design with co-evolutionary information retains protein function

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Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data

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Voxelized simulation of cerebral oxygen perfusion elucidates hypoxia in aged mouse cortex

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Four different mechanisms for switching cell polarity

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Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types

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A theory of memory for binary sequences: Evidence for a mental compression algorithm in humans

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Machine learning based CRISPR gRNA design for therapeutic exon skipping

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Assessing the potential impact of transmission during prolonged viral shedding on the effect of lockdown relaxation on COVID-19

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Aggregative cycles evolve as a solution to conflicts in social investment

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Predictions of COVID-19 dynamics in the UK: Short-term forecasting and analysis of potential exit strategies

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Mitochondrial depolarization promotes calcium alternans: Mechanistic insights from a ventricular myocyte model

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mbkmeans: Fast clustering for single cell data using mini-batch k-means

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Disease-driven reduction in human mobility influences human-mosquito contacts and dengue transmission dynamics

Kathryn L. Schaber, T. Alex Perkins, Alun L. Lloyd, Lance A. Waller, Uriel Kitron, Valerie A. Paz-Soldan, John P. Elder, Alan L. Rothman, David J. Civitello, William H. Elson, Amy C. Morrison, Thomas W. Scott, Gonzalo M. Vazquez-Prokopec

Sparse deep predictive coding captures contour integration capabilities of the early visual system

Victor Boutin, Angelo Franciosini, Frederic Chavane, Franck Ruffier, Laurent Perrinet

Modeling invasion patterns in the glioblastoma battlefield

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Catalytic promiscuity in the RNA World may have aided the evolution of prebiotic metabolism

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A reconstruction theory of relational schema induction

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The impact of interactions on invasion and colonization resistance in microbial communities

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PEtab—Interoperable specification of parameter estimation problems in systems biology

Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez, Lukas Refisch, Marcus Rosenblatt, Paul L. Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl

ProMod3—A versatile homology modelling toolbox

Gabriel Studer, Gerardo Tauriello, Stefan Bienert, Marco Biasini, Niklaus Johner, Torsten Schwede

A sensory integration account for time perception

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One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads

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Estimating the time-varying reproduction number of COVID-19 with a state-space method

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