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ORCIDPLoS Computational Biology, Volume 20
Volume 20, Number 1, January 2024
- Marcus Kaiser
:
Ten simple rules for establishing an experimental lab. - Gabriel Reuben Smith, Carolina Bello, Lalasia Bialic-Murphy, Emily Clark, Camille S. Delavaux, Camille Fournier de Lauriere, Johan van den Hoogen, Thomas Lauber, Haozhi Ma, Daniel S. Maynard, Matthew Mirman, Lidong Mo, Dominic Rebindaine, Josephine Elena Reek, Leland K. Werden, Zhaofei Wu, Gayoung Yang, Qingzhou Zhao, Constantin M. Zohner, Thomas Ward Crowther:
Ten simple rules for using large language models in science, version 1.0.
- Alice Bruel, Ignacio Abadía, Thibault Collin, Icare Sakr, Henri Lorach, Niceto R. Luque, Eduardo Ros, Auke Jan Ijspeert:
The spinal cord facilitates cerebellar upper limb motor learning and control; inputs from neuromusculoskeletal simulation. - Enrique R. Sebastian, Julio Esparza, Liset M. De La Prida:
Quantifying the distribution of feature values over data represented in arbitrary dimensional spaces. - Aakash Pandey, Abigail B. Feuka, Melinda Cosgrove, Megan Moriarty, Anthony Duffiney, Kurt C. Vercauteren, Henry Campa III, Kim M. Pepin:
Wildlife vaccination strategies for eliminating bovine tuberculosis in white-tailed deer populations. - Yoav Ger, Eliya Nachmani, Lior Wolf, Nitzan Shahar:
Harnessing the flexibility of neural networks to predict dynamic theoretical parameters underlying human choice behavior. - Jinchao Lv, Jin Wang, Chunhe Li:
Landscape quantifies the intermediate state and transition dynamics in ecological networks. - Yong-Jin Huang, Chun-Wei Chang, Chih-Hao Hsieh:
Detecting shifts in nonlinear dynamics using Empirical Dynamic Modeling with Nested-Library Analysis. - Jiarui Feng, S. Peter Goedegebuure, Amanda Zeng, Ye Bi, Ting Wang, Philip R. O. Payne, Li Ding, David DeNardo, William Hawkins, Ryan C. Fields, Fuhai Li:
sc2MeNetDrug: A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data. - Elizabeth Lawson-Keister, Tao Zhang, Fatemeh Nazari, François Fagotto, M. Lisa Manning:
Differences in boundary behavior in the 3D vertex and Voronoi models. - Lucas Castillo, Pablo León-Villagrá, Nick Chater, Adam Sanborn:
Explaining the flaws in human random generation as local sampling with momentum. - Haiqing Zhao, Hao Wu, Alex Guseman, Dulith Abeykoon, Christina M. Camara, Yamini Dalal, David Fushman, Garegin A. Papoian:
The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea. - Florian G. Pflug, Deepak Bhat, Simone Pigolotti:
Genome replication in asynchronously growing microbial populations. - Paul F. Lang, David R. Penas, Julio R. Banga, Daniel Weindl, Béla Novák:
Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells. - Chin-Hsuan Sophie Lin, Trang Thuy Do, Lee Unsworth, Marta I. Garrido:
Are we really Bayesian? Probabilistic inference shows sub-optimal knowledge transfer. - Tijl Grootswagers, Amanda K. Robinson, Sophia M. Shatek, Thomas A. Carlson:
Mapping the dynamics of visual feature coding: Insights into perception and integration. - Michael J. Plank, Leighton M. Watson, Oliver J. Maclaren:
Near-term forecasting of Covid-19 cases and hospitalisations in Aotearoa New Zealand. - Avik Mukherjee, Yu-Fang Chang, Yanqing Huang, Nina Catherine Benites, Leander Ammar, Jade Ealy, Mark Polk, Markus Basan:
Plasticity of growth laws tunes resource allocation strategies in bacteria. - Sjoerd Terpstra, Flavia Maria Darcie Marquitti, Vítor V. Vasconcelos:
Adaptive foraging of pollinators fosters gradual tipping under resource competition and rapid environmental change. - Christopher A. Mancuso, Kayla A. Johnson, Renming Liu, Arjun Krishnan:
Joint representation of molecular networks from multiple species improves gene classification. - Eric Elmoznino, Michael F. Bonner:
High-performing neural network models of visual cortex benefit from high latent dimensionality. - Jian Zou, Osama Shah, Yu-Chiao Chiu, Tianzhou Ma, Jennifer M. Atkinson, Steffi Oesterreich, Adrian V. Lee, George C. Tseng:
Systems approach for congruence and selection of cancer models towards precision medicine. - Eduardo Jardón-Valadez, Alfredo Ulloa-Aguirre:
Tracking conformational transitions of the gonadotropin hormone receptors in a bilayer of (SDPC) poly-unsaturated lipids from all-atom molecular dynamics simulations. - H. Robert Frost:
Tissue-adjusted pathway analysis of cancer (TPAC): A novel approach for quantifying tumor-specific gene set dysregulation relative to normal tissue. - Tyler S. Manning, Emma Alexander, Bruce G. Cumming, Gregory C. DeAngelis, Xin Huang, Emily A. Cooper:
Transformations of sensory information in the brain suggest changing criteria for optimality. - Karan Kabbur Hanumanthappa Manjunatha, Giorgia Baron, Danilo Benozzo, Erica Silvestri, Maurizio Corbetta, Alessandro Chiuso, Alessandra Bertoldo, Samir Suweis, Michele Allegra:
Controlling target brain regions by optimal selection of input nodes. - Kaiser J. Loell, Ryan Z. Friedman, Connie A. Myers, Joseph C. Corbo, Barak A. Cohen, Michael A. White:
Transcription factor interactions explain the context-dependent activity of CRX binding sites. - Hong An, J. Chris Pires, Gavin C. Conant:
Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression. - Janne J. Luppi, Cornelis J. Stam, Philip Scheltens, Willem de Haan:
Virtual neural network-guided optimization of non-invasive brain stimulation in Alzheimer's disease. - Maki Sudo, Koichi Fujimoto:
Diffusive mediator feedbacks control the health-to-disease transition of skin inflammation. - Giovanni Lo Iacono, Alasdair J. C. Cook, Gianne Derks, Lora E. Fleming, Nigel French, Emma L. Gillingham, Laura C. Gonzalez Villeta, Clare Heaviside, Roberto La Ragione, Giovanni Leonardi, Christophe E. Sarran, Sotiris Vardoulakis, Francis Senyah, Arnoud H. M. van Vliet, Gordon Nichols:
A mathematical, classical stratification modeling approach to disentangling the impact of weather on infectious diseases: A case study using spatio-temporally disaggregated Campylobacter surveillance data for England and Wales. - Martin Grunnill, Julien Arino, Zachary McCarthy, Nicola Luigi Bragazzi, Laurent Coudeville, Edward W. Thommes, Amine Amiche, Abbas Ghasemi, Lydia Bourouiba, Mohammadali Tofighi, Ali Asgary, Mortaza Baky-Haskuee, Jianhong Wu:
Modelling disease mitigation at mass gatherings: A case study of COVID-19 at the 2022 FIFA World Cup. - Shunsuke Koseki, Mitsuhiro Hayashibe, Dai Owaki:
Identifying essential factors for energy-efficient walking control across a wide range of velocities in reflex-based musculoskeletal systems. - Virginia Dominguez-Garcia, Sonia Kéfi:
The structure and robustness of ecological networks with two interaction types. - Sebastian Idesis, Sebastián Geli, Joshua Faskowitz, Jakub Vohryzek, Yonatan Sanz Perl, Florian Pieper, Edgar E. Galindo-Leon, Andreas K. Engel, Gustavo Deco:
Functional hierarchies in brain dynamics characterized by signal reversibility in ferret cortex. - Laura Schmid, Thomas Klotz, Oliver Röhrle, Randall K. Powers, Francesco Negro, Utku S. Yavuz:
Postinhibitory excitation in motoneurons can be facilitated by hyperpolarization-activated inward currents: A simulation study. - Anand Ramachandran, Steven S. Lumetta, Deming Chen:
PandoGen: Generating complete instances of future SARS-CoV-2 sequences using Deep Learning. - Chen Beer, Omri Barak:
Revealing and reshaping attractor dynamics in large networks of cortical neurons. - Sizhe Qiu, Xinlong Wan, Yueshan Liang, Cameron R. Lamoureux, Amir Akbari, Bernhard O. Palsson, Daniel C. Zielinski:
Inferred regulons are consistent with regulator binding sequences in E. coli. - Pablo Alvarez, Marouane El Mouss, Maxime Calka, Anca Belme, Gilles Berillon, Pauline Brige, Yohan Payan, Pascal Perrier, Amélie Vialet:
Predicting primate tongue morphology based on geometrical skull matching. A first step towards an application on fossil hominins. - Marine Louarn, Guillaume Collet, Ève Barré, Thierry Fest, Olivier Dameron, Anne Siegel, Fabrice Chatonnet:
Regulus infers signed regulatory relations from few samples' information using discretization and likelihood constraints. - Javier Robles, Ananth Prakash, Juan Antonio Vizcaíno, J. Ignacio Casal:
Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation. - Bryan Shin, Gary An, Chase Cockrell:
Examining B-cell dynamics and responsiveness in different inflammatory milieus using an agent-based model. - Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar:
A genome-wide comprehensive analysis of nucleosome positioning in yeast. - Pascal P. Klamser, Adrian Zachariae, Benjamin F. Maier, Olga Baranov, Clara Jongen, Frank Schlosser, Dirk Brockmann:
Inferring country-specific import risk of diseases from the world air transportation network. - Andrea Papale, David Holcman:
Chromatin phase separated nanoregions explored by polymer cross-linker models and reconstructed from single particle trajectories. - Kieran D. Lamb, Martha M. Luka, Megan Saathoff, Richard J. Orton, My V. T. Phan, Matthew Cotten, Ke Yuan, David L. Robertson:
Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. - Ian T. Ellwood:
Short-term Hebbian learning can implement transformer-like attention. - Raymond Copeland, Christopher Zhang, Brian K. Hammer, Peter J. Yunker:
Spatial constraints and stochastic seeding subvert microbial arms race. - Michiel van Boven, Christiaan H. van Dorp, Ilse Westerhof, Vincent Jaddoe, Valerie Heuvelman, Liesbeth Duijts, Elandri Fourie, Judith Sluiter-Post, Marlies A. van Houten, Paul Badoux, Sjoerd Euser, Bjorn Herpers, Dirk Eggink, Marieke de Hoog, Trisja Boom, Joanne Wildenbeest, Louis Bont, Ganna Rozhnova, Marc J. M. Bonten, Mirjam E. Kretzschmar, Patricia Bruijning-Verhagen:
Estimation of introduction and transmission rates of SARS-CoV-2 in a prospective household study. - David L. Krongauz, Amir Ayali, Gal A. Kaminka:
Vision-based collective motion: A locust-inspired reductionist model. - Mehran Fazli, Richard Bertram:
Conversion of spikers to bursters in pituitary cell networks: Is it better to disperse for maximum exposure or circle the wagons? - Beatriz Ocaña-Tienda, Odelaisy León-Triana, Julián Pérez-Beteta, Juan Jiménez-Sánchez, Víctor M. Pérez-García:
Radiation necrosis after radiation therapy treatment of brain metastases: A computational approach. - Ata Kalirad, Ralf J. Sommer:
Spatial and temporal heterogeneity alter the cost of plasticity in Pristionchus pacificus. - Magdalena Kozielska, Franz J. Weissing:
A neural network model for the evolution of learning in changing environments. - Yaojia Chen, Jiacheng Wang, Chunyu Wang, Quan Zou:
AutoEdge-CCP: A novel approach for predicting cancer-associated circRNAs and drugs based on automated edge embedding. - Louis Yat Hin Chan, Gunnar Rø, Jørgen Eriksson Midtbø, Francesco Di Ruscio, Sara Sofie Viksmoen Watle, Lene Kristine Juvet, Jasper Littmann, Preben Aavitsland, Karin Maria Nygård, Are Stuwitz Berg, Geir Bukholm, Anja Bråthen Kristoffersen, Kenth Engø-Monsen, Solveig Engebretsen, David Swanson, Alfonso Diz-Lois Palomares, Jonas Christoffer Lindstrøm, Arnoldo Frigessi, Birgitte Freiesleben de Blasio:
Modeling geographic vaccination strategies for COVID-19 in Norway.
- Paul J. N. Brodersen, Hannah Alfonsa, Lukas B. Krone, Cristina Blanco-Duque, Angus S. Fisk, Sarah J. Flaherty, Mathilde C. C. Guillaumin, Yi-Ge Huang, Martin C. Kahn, Laura E. McKillop, Linus Milinski, Lewis Taylor, Christopher W. Thomas, Tomoko Yamagata, Russell G. Foster, Vladyslav V. Vyazovskiy, Colin J. Akerman:
Somnotate: A probabilistic sleep stage classifier for studying vigilance state transitions. - Rituparna Samanta, Jeffrey J. Gray:
Implicit model to capture electrostatic features of membrane environment. - Said el Bouhaddani, Matthias Höllerhage, Hae-Won Uh, Claudia Moebius, Marc Bickle, Günter U. Höglinger, Jeanine J. Houwing-Duistermaat:
Statistical integration of multi-omics and drug screening data from cell lines.
- Sebastian Himbert, Dorian Gaboo, Emre Brookes, John F. Nagle, Maikel C. Rheinstädter:
MEDUSA: A cloud-based tool for the analysis of X-ray diffuse scattering to obtain the bending modulus from oriented membrane stacks. - Hua-Chang Chen, Jing Wang, Yu Shyr, Qi Liu:
FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing.
Volume 20, Number 2, February 2024
- Joachim Goedhart:
Studentsourcing - Aggregating and reusing data from a practical cell biology course.
- Helena Klara Jambor, Martin Bornhäuser:
Ten simple rules for designing graphical abstracts.
- Martijn A. de Jong, Esmée Adegeest, Noémie M. L. P. Bérenger-Currias, Maria Mircea, Roeland M. H. Merks, Stefan Semrau:
The shapes of elongating gastruloids are consistent with convergent extension driven by a combination of active cell crawling and differential adhesion. - Kameel Khabaz, Karen Yuan, Joseph Pugar, David Jiang, Seth Sankary, Sanjeev Dhara, Junsung Kim, Janet Kang, Nhung Nguyen, Kathleen Cao, Newell Washburn, Nicole Bohr, Cheong Jun Lee, Gordon Kindlmann, Ross Milner, Luka Pocivavsek:
The geometric evolution of aortic dissections: Predicting surgical success using fluctuations in integrated Gaussian curvature. - Jacob B. Roberts, Alberto A Nava, Allison N. Pearson, Matthew R. Incha, Luis E. Valencia, Melody Ma, Abhay Rao, Jay D. Keasling:
Foldy: An open-source web application for interactive protein structure analysis. - Sarah Percival, Joyce G. Onyenedum, Daniel H. Chitwood, Aman Y. Husbands:
Topological data analysis reveals core heteroblastic and ontogenetic programs embedded in leaves of grapevine (Vitaceae) and maracuyá (Passifloraceae). - Matthijs Pals, Jakob H. Macke, Omri Barak:
Trained recurrent neural networks develop phase-locked limit cycles in a working memory task. - Jane Knöchel, Charlotte Kloft, Wilhelm Huisinga:
Index analysis: An approach to understand signal transduction with application to the EGFR signalling pathway. - Etienne Thoret, Thomas Andrillon, Caroline Gauriau, Damien Léger, Daniel Pressnitzer:
Sleep deprivation detected by voice analysis. - Sarvenaz Sarabipour, Karina Kinghorn, Kaitlyn M. Quigley, Anita Kovacs-Kasa, Brian H. Annex, Victoria L. Bautch, Feilim Mac Gabhann:
Trafficking dynamics of VEGFR1, VEGFR2, and NRP1 in human endothelial cells. - Connor R. King, Casey-Tyler Berezin, Jean Peccoud:
Stochastic model of vesicular stomatitis virus replication reveals mutational effects on virion production. - Te Liu, Sichao Huang, Qian Zhang, Yu Xia, Manjie Zhang, Bin Sun:
Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data. - Yu Feng, Nicolas Brunel:
Attractor neural networks with double well synapses. - Keith E. Kennedy, Nicole Kerlero de Rosbo, Antonio Uccelli, Maria Cellerino, Federico Ivaldi, Paola Contini, Raffaele De Palma, Hanne F. Harbo, Tone Berge, Steffan D. Bos, Einar A. Høgestøl, Synne Brune-Ingebretsen, Sigrid A. de Rodez Benavent, Friedemann Paul, Alexander U. Brandt, Priscilla Bäcker-Koduah, Janina Behrens, Joseph Kuchling, Susanna Asseyer, Michael Scheel, Claudia Chien, Hanna Zimmermann, Seyedamirhosein Motamedi, Josef Kauer-Bonin, Julio Saez-Rodriguez, Melanie Rinas, Leonidas G. Alexopoulos, Magí Andorrà, Sara Llufriu, Albert Saiz, Yolanda Blanco, Eloy Martinez-Heras, Elisabeth Solana, Irene Pulido-Valdeolivas, Elena H. Martinez-Lapiscina, Jordi García-Ojalvo, Pablo Villoslada:
Multiscale networks in multiple sclerosis. - Zhijie Feng, Robert Marsland III, Jason W. Rocks, Pankaj Mehta:
Emergent competition shapes top-down versus bottom-up control in multi-trophic ecosystems. - Joe Hilton, Ian M. Hall:
A beta-Poisson model for infectious disease transmission. - Josepha Godivier, Elizabeth A. Lawrence, Mengdi Wang, Chrissy L. Hammond, Niamh C. Nowlan:
Compressive stress gradients direct mechanoregulation of anisotropic growth in the zebrafish jaw joint. - Linxing Preston Jiang, Rajesh P. N. Rao:
Dynamic predictive coding: A model of hierarchical sequence learning and prediction in the neocortex. - Xiang Liu, Nancy Gillis, Chang Jiang, Anthony McCofie, Timothy I. Shaw, Aik Choon Tan, Bo Zhao, Lixin Wan, Derek R. Duckett, Mingxiang Teng:
An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level. - Meenal Datta, McCarthy Kennedy, Saeed Siri, Laura E. Via, James W. Baish, Lei Xu, Véronique Dartois, Clifton E. Barry 3rd, Rakesh K. Jain:
Mathematical model of oxygen, nutrient, and drug transport in tuberculosis granulomas. - Samuel H. A. von der Dunk, Paulien Hogeweg, Berend Snel:
Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis. - Nathan LaPierre, Harold Pimentel:
Accounting for isoform expression increases power to identify genetic regulation of gene expression. - Kemin Zhu, Ling Yin, Kang Liu, Junli Liu, Yepeng Shi, Xuan Li, Hongyang Zou, Huibin Du:
Generating synthetic population for simulating the spatiotemporal dynamics of epidemics. - Carlos S. N. Brito, Wulfram Gerstner:
Learning what matters: Synaptic plasticity with invariance to second-order input correlations. - Zhenxing Guo, Daoyu Duan, Wen Tang, Julia Zhu, William S. Bush, Liangliang Zhang, Xiaofeng Zhu, Fulai Jin, Hao Feng:
magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing. - Lachlan Baer, Karissa Barthelson, John H. Postlethwait, David L. Adelson, Stephen M. Pederson, Michael Lardelli:
Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis. - Jiao Zhao, Ke Chen, Bernhard O. Palsson, Laurence Yang:
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. - Li-Dunn Chen, Michael A. Caprio, Devin M. Chen, Andrew J. Kouba, Carrie K. Kouba:
Enhancing predictive performance for spectroscopic studies in wildlife science through a multi-model approach: A case study for species classification of live amphibians. - Jakub Köry, Vedang Narain, Bernadette J. Stolz, Jakob Kaeppler, Bostjan Markelc, Ruth J. Muschel, Philip K. Maini, Joe Pitt-Francis, Helen M. Byrne:
Enhanced perfusion following exposure to radiotherapy: A theoretical investigation. - András Zeke, Toby J. Gibson, Laszlo Dobson:
Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents. - Martin L. L. R. Barry, Wulfram Gerstner:
Fast adaptation to rule switching using neuronal surprise. - Sven Wientjes, Clay B. Holroyd:
The successor representation subserves hierarchical abstraction for goal-directed behavior. - Alexander D. Bird, Hermann Cuntz, Peter Jedlicka:
Robust and consistent measures of pattern separation based on information theory and demonstrated in the dentate gyrus. - Jose Gabriel Nino Barreat, Aris Katzourakis:
Ecological and evolutionary dynamics of cell-virus-virophage systems. - Natalie Schieferstein, Tilo Schwalger, Benjamin Lindner, Richard Kempter:
Intra-ripple frequency accommodation in an inhibitory network model for hippocampal ripple oscillations. - Francesco Pinotti, José Lourenço, Sunetra Gupta, Suman Das Gupta, Joerg Henning, Damer Blake, Fiona Tomley, Tony Barnett, Dirk Pfeiffer, Md. Ahasanul Hoque, Guillaume Fournié:
EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks. - Quintessa Hay, Christopher Grubb, Sarah Minucci, Michael S. Valentine, Jennifer Van Mullekom, Rebecca L. Heise, Angela M. Reynolds:
Age-dependent ventilator-induced lung injury: Mathematical modeling, experimental data, and statistical analysis. - Juliette Cooke, Maxime Delmas, Cecilia Wieder, Pablo Rodríguez-Mier, Clément Frainay, Florence Vinson, Timothy M. D. Ebbels, Nathalie Poupin, Fabien Jourdan:
Genome scale metabolic network modelling for metabolic profile predictions. - Eshan S. King, Dagim Shiferaw Tadele, Beck Pierce, Michael Hinczewski, Jacob G. Scott:
Diverse mutant selection windows shape spatial heterogeneity in evolving populations. - Tom Van Wouwe, Jennifer L. Hicks, Scott L. Delp, C. Karen Liu:
A simulation framework to determine optimal strength training and musculoskeletal geometry for sprinting and distance running. - Tomas Barta, Lubomir Kostal:
Shared input and recurrency in neural networks for metabolically efficient information transmission. - Moritz Groden, Hannah M. Moessinger, Barbara Schaffran, Javier DeFelipe, Ruth Benavides-Piccione, Hermann Cuntz, Peter Jedlicka:
A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites. - Nicholas Tolley, Pedro L. C. Rodrigues, Alexandre Gramfort, Stephanie R. Jones:
Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference. - Paul Soulos, Leyla Isik:
Disentangled deep generative models reveal coding principles of the human face processing network. - Pan Li, Jae Kyoung Kim:
Circadian regulation of sinoatrial nodal cell pacemaking function: Dissecting the roles of autonomic control, body temperature, and local circadian rhythmicity.