PLoS Comput. Biol.

Publications

volume 20, number 2, 2024

Paul Soulos, Leyla Isik
Disentangled deep generative models reveal coding principles of the human face processing network. PLoS Comput. Biol. 20 (2) (2024)
Helena Klara Jambor, Martin Bornhäuser
Ten simple rules for designing graphical abstracts. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
Aaron L. Phillips, Scott Ferguson, Rachel A. Burton, Nathan S. Watson-Haigh
CLAW: An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
Daniele Dall'Olio, Eric Sträng, Amin T. Turki, Jesse M. Tettero, Martje Barbus, Renate Schulze-Rath, Javier Martinez Elicegui, Tommaso Matteuzzi, Alessandra Merlotti, Luciana Carota, Claudia Sala, Matteo G. Della Porta, Enrico Giampieri, Jesús María Hernández-Rivas, Lars Bullinger, Gastone C. Castellani
Covering Hierarchical Dirichlet Mixture Models on binary data to enhance genomic stratifications in onco-hematology. PLoS Comput. Biol. 20 (2) (2024)
Jane Knöchel, Charlotte Kloft, Wilhelm Huisinga
Index analysis: An approach to understand signal transduction with application to the EGFR signalling pathway. PLoS Comput. Biol. 20 (2) (2024)
Alexander Borst
Connectivity Matrix Seriation via Relaxation. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
R. Dustin Schaeffer, Jing Zhang, Kirill E. Medvedev, Lisa N. Kinch, Qian Cong, Nick V. Grishin
ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
Yu Feng, Nicolas Brunel
Attractor neural networks with double well synapses. PLoS Comput. Biol. 20 (2) (2024)
Joe Hilton, Ian M. Hall
A beta-Poisson model for infectious disease transmission. PLoS Comput. Biol. 20 (2) (2024)
Alexander D. Bird, Hermann Cuntz, Peter Jedlicka
Robust and consistent measures of pattern separation based on information theory and demonstrated in the dentate gyrus. PLoS Comput. Biol. 20 (2) (2024)
Natalie Schieferstein, Tilo Schwalger, Benjamin Lindner, Richard Kempter
Intra-ripple frequency accommodation in an inhibitory network model for hippocampal ripple oscillations. PLoS Comput. Biol. 20 (2) (2024)
Sangjeong Lee, Hyunwoo Kim
Bidirectional de novo peptide sequencing using a transformer model. PLoS Comput. Biol. 20 (2) (2024)
Eshan S. King, Dagim S. Tadele, Beck Pierce, Michael Hinczewski, Jacob G. Scott
Diverse mutant selection windows shape spatial heterogeneity in evolving populations. PLoS Comput. Biol. 20 (2) (2024)
Linxing Preston Jiang, Rajesh P. N. Rao
Dynamic predictive coding: A model of hierarchical sequence learning and prediction in the neocortex. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
Hong Seo Lim, Peng Qiu
Quantifying the clusterness and trajectoriness of single-cell RNA-seq data. PLoS Comput. Biol. 20 (2) (2024)
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). PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
Tyson L. Swetnam, Parker B. Antin, Ryan Bartelme, Alexander Bucksch, David Camhy, Greg Chism, Illyoung Choi, Amanda M. Cooksey, Michele Cosi, Cindy Cowen, Michael Culshaw-Maurer, Robert Davey, Sean Davey, Upendra Devisetty, Tony Edgin, Andy Edmonds, Dmitry V. Fedorov, Jeremy Frady, John Fonner, Jeffrey K. Gillan, Iqbal Hossain, Blake Joyce, Konrad Lang, Tina Lee, Shelley Littin, Ian McEwen, Nirav C. Merchant, David Micklos, Andrew Nelson, Ashley Ramsey, Sarah Roberts, Paul Sarando, Edwin Skidmore, Jawon Song, Mary Margaret Sprinkle, Sriram Srinivasan, Dan Stanzione, Jonathan D. Strootman, Sarah Stryeck, Reetu Tuteja, Matthew Vaughn, Mojib Wali, Mariah Wall, Ramona Walls, Liya Wang, Todd Wickizer, Jason Williams, John Wregglesworth, Eric Lyons
CyVerse: Cyberinfrastructure for open science. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
Samuel H. A. von der Dunk, Paulien Hogeweg, Berend Snel
Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
Bastiaan J. R. Cockx, Tim Foster, Robert J. Clegg, Kieran Alden, Sankalp Arya, Dov J. Stekel, Barth F. Smets, Jan-Ulrich Kreft
Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0. PLoS Comput. Biol. 20 (2) (2024)
Yongtao Ye, Marcus H. Shum, Joseph L. Tsui, Guangchuang Yu, David K. Smith, Huachen Zhu, Joseph T. Wu, Yi Guan, Tommy Tsan-Yuk Lam
Robust expansion of phylogeny for fast-growing genome sequence data. PLoS Comput. Biol. 20 (2) (2024)
Takahiro Kohsokabe, Shigeru Kuratanai, Kunihiko Kaneko
Developmental hourglass: Verification by numerical evolution and elucidation by dynamical-systems theory. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
Joachim Goedhart
Studentsourcing - Aggregating and reusing data from a practical cell biology course. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
Chen Zhang, Junhui Gao, Hong-Yu Chen, Lingxin Kong, Guangshuo Cao, Xiangyu Guo, Wei Liu, Bin Ren, Dong-Qing Wei
STGIC: A graph and image convolution-based method for spatial transcriptomic clustering. PLoS Comput. Biol. 20 (2) (2024)
Denise Vlachou, Maria Veretennikova, Laura Usselmann, Vadim Vasilyev, Sascha Ott, Georg A. Bjarnason, Robert Dallmann, Francis Levi, David A. Rand
TimeTeller: A tool to probe the circadian clock as a multigene dynamical system. PLoS Comput. Biol. 20 (2) (2024)
Luca Sesta, Andrea Pagnani, Jorge Fernandez-de-Cossío-Diaz, Guido Uguzzoni
Inference of annealed protein fitness landscapes with AnnealDCA. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)
Connor R. King, Casey-Tyler Berezin, Jean Peccoud
Stochastic model of vesicular stomatitis virus replication reveals mutational effects on virion production. PLoS Comput. Biol. 20 (2) (2024)
Lily Monnier, Paul-Henry Cournède
A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization. PLoS Comput. Biol. 20 (2) (2024)
Carlos S. N. Brito, Wulfram Gerstner
Learning what matters: Synaptic plasticity with invariance to second-order input correlations. PLoS Comput. Biol. 20 (2) (2024)
Sven Wientjes, Clay B. Holroyd
The successor representation subserves hierarchical abstraction for goal-directed behavior. PLoS Comput. Biol. 20 (2) (2024)
Jiao Zhao, Ke Chen, Bernhard O. Palsson, Laurence Yang
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. PLoS Comput. Biol. 20 (2) (2024)
Bonnie V. Dougherty, Connor J. Moore, Kristopher D. Rawls, Matthew L. Jenior, Bryan Chun, Sarbajeet Nagdas, Jeffrey J. Saucerman, Glynis L. Kolling, Anders Wallqvist, Jason A. Papin
Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism. PLoS Comput. Biol. 20 (2) (2024)
Dennis Eschweiler, Rüveyda Yilmaz, Matisse Baumann, Ina Laube, Rijo Roy, Abin Jose, Daniel Brückner, Johannes Stegmaier
Denoising diffusion probabilistic models for generation of realistic fully-annotated microscopy image datasets. PLoS Comput. Biol. 20 (2) (2024)
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. PLoS Comput. Biol. 20 (2) (2024)