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ORCIDPLoS Computational Biology, Volume 21
Volume 21, Number 1, 2025
- Alice Bruel
, Lina Bacha, Emma Boehly, Constance De Trogoff, Luca Represa, Grégoire Courtine, Auke Jan Ijspeert:
Role and modulation of various spinal pathways for human upper limb control in different gravity conditions. 1012069 - Alessandro Pazzaglia, Andrej Bicanski, Andrea Ferrario, Jonathan Arreguit, Dimitri Ryczko, Auke Jan Ijspeert:
Balancing central control and sensory feedback produces adaptable and robust locomotor patterns in a spiking, neuromechanical model of the salamander spinal cord. 1012101 - Glen McLachlan, Piotr Majdak, Jonas Reijniers, Michael Mihocic, Herbert Peremans:
Bayesian active sound localisation: To what extent do humans perform like an ideal-observer? 1012108 - Luis L. Fonseca, Lucas Böttcher, Borna Mehrad, Reinhard C. Laubenbacher:
Optimal control of agent-based models via surrogate modeling. 1012138 - Evan Gorstein, Rosa Aghdam, Claudia R. Solís-Lemus:
HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data. 1012143 - Magnus Pirovino, Christian Iseli, Joseph A. Curran, Bernard Conrad:
Biomathematical enzyme kinetics model of prebiotic autocatalytic RNA networks: degenerating parasite-specific hyperparasite catalysts confer parasite resistance and herald the birth of molecular immunity. 1012162 - Max de Rooij, Balázs Erdos, Natal A. W. van Riel, Shauna D. O'Donovan:
Physiology-informed regularisation enables training of universal differential equation systems for biological applications. 1012198 - Alexander G. Ginsberg, Scott F. Lempka, Bo Duan, Victoria Booth, Jennifer Crodelle:
Mechanisms for dysregulation of excitatory-inhibitory balance underlying allodynia in dorsal horn neural subcircuits. 1012234 - Xuexing Du, Jennifer Crodelle, Victor J. Barranca, Songting Li, Yunzhu Shi, Shangbang Gao, Douglas Zhou:
Biophysical modeling and experimental analysis of the dynamics of C. elegans body-wall muscle cells. 1012318 - Oane Gros, Josiah B. Passmore, Noa O. Borst, Dominik Kutra, Wilco Nijenhuis, Timothy Fuqua, Lukas C. Kapitein, Justin M. Crocker, Anna Kreshuk, Simone Köhler:
Spherical harmonics texture extraction for versatile analysis of biological objects. 1012349 - Chunhong Long, Hongqiong Liang, Biao Wan:
DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study. 1012362 - Kwang Su Kim, Masashi Iwamoto, Kosaku Kitagawa, Hyeongki Park, Sanae Hayashi, Senko Tsukuda, Takeshi Matsui, Masanori Atsukawa, Kentaro Matsuura, Natthaya Chuaypen, Pisit Tangkijvanich, Lena Allweiss, Takara Nishiyama, Naotoshi Nakamura, Yasuhisa Fujita, Eiryo Kawakami, Shinji Nakaoka, Masamichi Muramatsu, Kazuyuki Aihara, Takaji Wakita, Alan S. Perelson, Maura Dandri, Koichi Watashi, Shingo Iwami, Yasuhito Tanaka:
Prediction of cccDNA dynamics in hepatitis B patients by a combination of serum surrogate markers. 1012615 - Yulong Kan, Yunjing Qi, Zhongxiao Zhang, Xikeng Liang, Weihao Wang, Shuilin Jin:
Integration of unpaired single cell omics data by deep transfer graph convolutional network. 1012625 - Kevin P. Greenman, Ava P. Amini, Kevin K. Yang:
Benchmarking uncertainty quantification for protein engineering. 1012639 - Amrit Bagchi, Bapi Sarker, Jialiang Zhang, Marcus Foston, Amit Pathak:
Fast yet force-effective mode of supracellular collective cell migration due to extracellular force transmission. 1012664 - Arif Badrou, Crystal A. Mariano, Gustavo O. Ramirez, Matthew Shankel, Nuno Rebelo, Mona Eskandari:
Towards constructing a generalized structural 3D breathing human lung model based on experimental volumes, pressures, and strains. 1012680 - Julien Laussu, Deborah Michel, Léa Magne, Stéphane Segonds, Steven Marguet, Dimitri Hamel, Muriel Quaranta-Nicaise, Frederick Barreau, Emmanuel Mas, Vincent Velay, Florian Bugarin, Audrey Ferrand:
Deciphering the interplay between biology and physics with a finite element method-implemented vertex organoid model: A tool for the mechanical analysis of cell behavior on a spherical organoid shell. 1012681 - Obaï B. K. Ali, Alexandre Vidal, Christophe Grova, Habib Benali:
Dialogue mechanisms between astrocytic and neuronal networks: A whole-brain modelling approach. 1012683 - Hidekazu Hishinuma, Hisako Takigawa-Imamura, Takashi Miura:
Data-driven discovery and parameter estimation of mathematical models in biological pattern formation. 1012689 - Azusa Tanaka, Yasuhiro Ishitsuka, Hiroki Ohta, Norihiro Takenouchi, Masanori Nakagawa, Ki-Ryang Koh, Chiho Onishi, Hiromitsu Tanaka, Akihiro Fujimoto, Jun-ichirou Yasunaga, Masao Matsuoka:
Integrative analysis of ATAC-seq and RNA-seq for cells infected by human T-cell leukemia virus type 1. 1012690 - Remy Ben Messaoud, Vincent Le Du, Camile Bousfiha, Marie-Constance Corsi, Juliana Gonzalez-Astudillo, Brigitte Charlotte Kaufmann, Tristan Venot, Baptiste Couvy-Duchesne, Lara Migliaccio, Charlotte Rosso, Paolo Bartolomeo, Mario Chavez, Fabrizio de Vico Fallani:
Low-dimensional controllability of brain networks. 1012691 - Ismael Kherroubi Garcia, Christopher Erdmann, Sandra Gesing, C. Michael Barton, Lauren Cadwallader, Geerten M. Hengeveld, Christine R. Kirkpatrick, Kathryn Knight, Carsten Lemmen, Rebecca Ringuette, Qing Zhan, Melissa Harrison, Feilim Mac Gabhann, Natalie Meyers, Cailean Osborne, Charlotte Till, Paul R. Brenner, Matt Buys, Min Chen, Allen Lee, Jason A. Papin, Yuhan Rao:
Ten simple rules for good model-sharing practices. 1012702 - Soham Mandal, Ann-Marie Baker, Trevor A. Graham, Konstantin Bräutigam:
The tumour histopathology "glossary" for AI developers. 1012708 - Asgeir Kobro-Flatmoen, Stig W. Omholt:
Intraneuronal binding of amyloid beta with reelin - Implications for the onset of Alzheimer's disease. 1012709 - Luca Oneto, Davide Chicco:
Eight quick tips for biologically and medically informed machine learning. 1012711 - Mohammad Neamul Kabir, Li Rong Wang, Wilson Wen Bin Goh:
Exploiting the similarity of dissimilarities for biomedical applications and enhanced machine learning. 1012716 - Shoutik Mukherjee, Behtash Babadi, Shihab A. Shamma:
Sparse high-dimensional decomposition of non-primary auditory cortical receptive fields. 1012721 - Nan Wu, Zhi-Chao Xu, Kai-Dong Du, Shen Huang, Naohiro Kobayashi, Yutaka Kuroda, Yan-Hong Bai:
A Structural Model of Truncated Gaussia princeps Luciferase Elucidating the Crucial Catalytic Function of No.76 Arginine towards Coelenterazine Oxidation. 1012722 - Francisco Páscoa dos Santos, Paul F. M. J. Verschure:
Excitatory-inhibitory homeostasis and bifurcation control in the Wilson-Cowan model of cortical dynamics. 1012723 - María Ruiz Ortega, Mikhail V. Pogorelyy, Anastasia A. Minervina, Paul G. Thomas, Thierry Mora, Aleksandra M. Walczak:
Learning predictive signatures of HLA type from T-cell repertoires. 1012724 - Zeinab Mousavi, Marios Arvanitis, Thuyvy Duong, Jennifer A. Brody, Alexis Battle, Nona Sotoodehnia, Ali Shojaie, Dan E. Arking, Joel S. Bader:
Prioritization of causal genes from genome-wide association studies by Bayesian data integration across loci. 1012725 - Diego Tec-Campos, Juan D. Tibocha-Bonilla, Celina Jiang, Anurag Passi, Deepan Thiruppathy, Cristal Zuñiga, Camila Posadas, Alejandro Zepeda, Karsten Zengler:
A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers. 1012736 - Alejandro Feito, Ignacio Sanchez-Burgos, Ignacio Tejero, Eduardo Sanz, Antonio Rey, Rosana Collepardo-Guevara, Andres R. Tejedor, Jorge R. Espinosa:
Benchmarking residue-resolution protein coarse-grained models for simulations of biomolecular condensates. 1012737 - Xiaoyi Wang, Zhen Jin:
Multi-region infectious disease prediction modeling based on spatio-temporal graph neural network and the dynamic model. 1012738 - Lulu Pan, Qian Gao, Kecheng Wei, Yongfu Yu, Guoyou Qin, Tong Wang:
A robust transfer learning approach for high-dimensional linear regression to support integration of multi-source gene expression data. 1012739 - Nicole M. Moody, Cole M. Williams, Sohini Ramachandran, Matthew J. Fuxjager:
Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense. 1012740 - Natalie R. Davidson, Fan Zhang, Casey S. Greene:
BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk. 1012742 - Peng Ren, Xuehua Cui, Xia Liang:
Connectome-based biophysical models of pathological protein spreading in neurodegenerative diseases. 1012743 - Chuanmei Bi, Yong Shi, Junfeng Xia, Zhen Liang, Zhiqiang Wu, Kai Xu, Na Cheng:
Ensemble learning-based predictor for driver synonymous mutation with sequence representation. 1012744 - Jiang Mao, Constantin A Rothkopf, Alan A. Stocker:
Adaptation optimizes sensory encoding for future stimuli. 1012746 - Yunyun Dong, Yuanrong Zhang, Yuhua Qian, Yiming Zhao, Ziting Yang, Xiufang Feng:
ASGCL: Adaptive Sparse Mapping-based graph contrastive learning network for cancer drug response prediction. 1012748 - Lucas Böttcher, Maria R. D'Orsogna, Tom Chou:
Aggregating multiple test results to improve medical decision-making. 1012749 - Xu Shi, Xiao Wang, Lu Jin, Leena Halakivi-Clarke, Robert Clarke, Andrew F. Neuwald, Jianhua Xuan:
Bayesian identification of differentially expressed isoforms using a novel joint model of RNA-seq data. 1012750 - Pranjul Gupta, Katharina Dobs:
Human-like face pareidolia emerges in deep neural networks optimized for face and object recognition. 1012751 - Meichen Fang, Gennady Gorin, Lior Pachter:
Trajectory inference from single-cell genomics data with a process time model. 1012752 - Toviah Moldwin, Li Shay Azran, Idan Segev:
The calcitron: A simple neuron model that implements many learning rules via the calcium control hypothesis. 1012754 - Ahmed Daoud, Asa Ben-Hur:
The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models. 1012755 - Edoardo Saccenti, Cristina Furlan:
Ten simple rules to complete successfully a computational MSc thesis project. 1012756 - Xiaojun Wu, Meilu McDermott, Adam L. Maclean:
Data-driven model discovery and model selection for noisy biological systems. 1012762 - Fernando A. Najman, Antonio Galves, Marcela Svarc, Claudia D. Vargas:
Extracting the fingerprints of sequences of random rhythmic auditory stimuli from electrophysiological data. 1012765 - Matthew Gerry, Duncan Kirby, Boian S. Alexandrov, Dvira Segal, Anton Zilman:
Specificity and tunability of efflux pumps: A new role for the proton gradient? 1012772 - Giovanni di Sarra, Siddharth Jha, Yasser Roudi:
The role of oscillations in grid cells' toroidal topology. 1012776 - Phoebe Asplin, Matt J. Keeling, Rebecca Mancy, Edward M. Hill:
Correction: Epidemiological and health economic implications of symptom propagation in respiratory pathogens: A mathematical modelling investigation. 1012791
Volume 21, Number 2, 2025
- Alexandra Teslya, Janneke C. M. Heijne, Maarten F. Schim van der Loeff, Ard van Sighem, Jacob Aiden Roberts, Maartje Dijkstra, Godelieve J. de Bree, Axel J. Schmidt, Kai J. Jonas, Mirjam E. Kretzschmar, Ganna Rozhnova:
Impact of increased diagnosis of early HIV infection and immediate antiretroviral treatment initiation on HIV transmission among men who have sex with men in the Netherlands. 1012055 - Christina Y. Lee, Sina Bonakdar, Kelly B. Arnold:
An in silico framework for the rational design of vaginal probiotic therapy. 1012064 - Alexa Aucoin, Kevin K. Lin, Katalin M. Gothard:
Detection of latent brain states from spontaneous neural activity in the amygdala. 1012247 - Yanru Jiang, Rick Dale:
Mapping the learning curves of deep learning networks. 1012286 - Alexander R. Kaye, Giorgio Guzzetta, Michael J. Tildesley, Robin N. Thompson:
Quantifying infectious disease epidemic risks: A practical approach for seasonal pathogens. 1012364 - Sara Ershadmanesh, Sahar Rajabi, Reza Rostami, Rani Moran, Peter Dayan:
Noradrenergic and Dopaminergic modulation of meta-cognition and meta-control. 1012675 - Mai Chan Lau, Jennifer Borowsky, Juha P. Väyrynen, Koichiro Haruki, Melissa Zhao, Andressa Dias Costa, Simeng Gu, Annacarolina Da Silva, Tomotaka Ugai, Kota Arima, Minh N. Nguyen, Yasutoshi Takashima, Joe Yeong, David Tai, Tsuyoshi Hamada, Jochen K. Lennerz, Charles S. Fuchs, Catherine J. Wu, Jeffrey A. Meyerhardt, Shuji Ogino, Jonathan A. Nowak:
Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment. 1012707 - Xueda Shen, Aaron Rumack, Bryan Wilder, Ryan J. Tibshirani:
Nowcasting reported covid-19 hospitalizations using de-identified, aggregated medical insurance claims data. 1012717 - Timothée Poisot, Daniel J. Becker, Cole B. Brookson, Ellie Graeden, Sadie J. Ryan, Gemma Turon, Colin J. Carlson:
Ten quick tips to build a Model Life Cycle. 1012731 - Jan-Simon Baasner, Andreas Rempel, Dakota Howard, Boas Pucker:
NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction. 1012732 - Luca Musella, Alejandro Afonso Castro, Xin Lai, Max Widmann, Julio Vera:
ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature. 1012745 - Eliezyer Fermino de Oliveira, Pranjal Garg, Jens Hjerling-Leffler, Renata Batista-Brito, Lucas Sjulson:
Identifying patterns differing between high-dimensional datasets with generalized contrastive PCA. 1012747 - Grace C. McKenzie-Smith, Scott W. Wolf, Julien F. Ayroles, Joshua W. Shaevitz:
Capturing continuous, long timescale behavioral changes in Drosophila melanogaster postural data. 1012753 - Dennis Khodasevich, Nina Holland, Lars van der Laan, Andrés Cárdenas:
A SuperLearner-based pipeline for the development of DNA methylation-derived predictors of phenotypic traits. 1012768 - Jordan Childs, Tiago Bernardino Gomes, Amy E. Vincent, Andrew Golightly, Conor Lawless:
Bayesian classification of OXPHOS deficient skeletal myofibres. 1012770 - Rui Miao, Hao-Yang Yu, Bing-Jie Zhong, Hong-Xia Sun, Qiang Xia:
AWGE-ESPCA: An edge sparse PCA model based on adaptive noise elimination regularization and weighted gene network for Hermetia illucens genomic data analysis. 1012773 - Nathanaël Hozé, Margarita Pons-Salort, C. Jessica E. Metcalf, Michael White, Henrik Salje, Simon Cauchemez:
RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies. 1012777 - Wenxuan Li, Xu Chen, Suli Liu, Chiyu Zhang, Guyue Liu:
Using a multi-strain infectious disease model with physical information neural networks to study the time dependence of SARS-CoV-2 variants of concern. 1012778 - Justin Sheen, Lee Kennedy-Shaffer, Michael Z. Levy, C. Jessica E. Metcalf:
Design of field trials for the evaluation of transmissible vaccines in animal populations. 1012779 - Brinkley Raynor, Elvis W. Díaz, Micaela De la Puente-León, Maria T. Rieders, Sergio E. Recuenco, Michael Z. Levy, Ricardo Castillo-Neyra:
Challenging a paradigm: Staggered versus single-pulse mass dog vaccination strategy for rabies elimination. 1012780 - Rachel Russell, Nik J. Cunniffe:
Optimal control prevents itself from eradicating stochastic disease epidemics. 1012781 - Shan Gao, Amit K. Chakraborty, Russell Greiner, Mark A. Lewis, Hao Wang:
Early detection of disease outbreaks and non-outbreaks using incidence data: A framework using feature-based time series classification and machine learning. 1012782 - Matthias C. Rillig:
Ten simple rules for fostering creativity in research labs. 1012788 - Lars Berling, Jonathan Klawitter, Remco R. Bouckaert, Dong Xie, Alex Gavryushkin, Alexei J. Drummond:
Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities. 1012789 - Belinda Lombard, Harry Moultrie, Juliet R. C. Pulliam, Cari van Schalkwyk:
Simulation-based validation of a method to detect changes in SARS-CoV-2 reinfection risk. 1012792 - Jacopo Marchi, Chau Nguyen Ngoc Minh, Laurent Debarbieux, Joshua S. Weitz:
Multi-strain phage induced clearance of bacterial infections. 1012793 - Niklas Brake, Anmar Khadra:
Contributions of action potentials to scalp EEG: Theory and biophysical simulations. 1012794 - Pasquale Casaburi, Lorenzo Dall'Amico, Nicolò Gozzi, Kyriaki Kalimeri, Anna Sapienza, Rossano Schifanella, T. Di Matteo, Leo Ferres, Mattia Mazzoli:
Resilience of mobility network to dynamic population response across COVID-19 interventions: Evidences from Chile. 1012802 - Xianghao Zhan, Qinmei Xu, Yuanning Zheng, Guangming Lu, Olivier Gevaert:
Reliability-enhanced data cleaning in biomedical machine learning using inductive conformal prediction. 1012803 - Vemund Sigmundson Schøyen, Kosio Beshkov, Markus Pettersen, Erik Hermansen, Konstantin Holzhausen, Anders Malthe-Sørenssen, Marianne Fyhn, Mikkel Elle Lepperød:
Hexagons all the way down: grid cells as a conformal isometric map of space. 1012804 - Christopher Graser, Takako Fujiwara-Greve, Julián García, Matthijs van Veelen:
Repeated games with partner choice. 1012810 - Shan Zhong, Nader Pouratian, Vassilios N. Christopoulos:
Computational mechanism underlying switching of motor actions. 1012811 - Jamel Simpson, Peter M. Kasson:
Structural prediction of chimeric immunogen candidates to elicit targeted antibodies against betacoronaviruses. 1012812 - Shun Wang, Jinzhi Lei, Xiufen Zou, Suoqin Jin:
Integrating multiscale mathematical modeling and multidimensional data reveals the effects of epigenetic instability on acquired drug resistance in cancer. 1012815 - Rodrigo Osuna-Orozco, Edward Castillo, Kameron Decker Harris, Samantha R. Santacruz:
Identification of recurrent dynamics in distributed neural populations. 1012816 - Ines S. C. Baptista, Suchintak Dash, Amir M. Arsh, Vinodh Kandavalli, Carlo Maria Scandolo, Barry C. Sanders, Andre S. Ribeiro:
Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses. 1012817 - Fatemeh Kamali, Amir Abolfazl Suratgar, Mohammad Bagher Menhaj, Reza Abbasi-Asl:
Compression-enabled interpretability of voxelwise encoding models. 1012822 - Nicolas Banholzer, Keren Middelkoop, Juane Leukes, Ernest Weingartner, Remo Schmutz, Kathrin Zürcher, Matthias Egger, Robin Wood, Lukas Fenner:
Estimating Mycobacterium tuberculosis transmission in a South African clinic: Spatiotemporal model based on person movements. 1012823 - Paulina N. Smaruj, Fahad Kamulegeya, David R. Kelley, Geoffrey Fudenberg:
Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2. 1012824 - Daipeng Chen, Xinxin Liu, Haijiang Wang, Roeland M. H. Merks, David A. Baker:
A model of Notch signalling control of angiogenesis: Evidence of a role for Notch ligand heterodimerization. 1012825 - Subhadip Biswas, Davit A. Potoyan:
Decoding biomolecular condensate dynamics: an energy landscape approach. 1012826 - Laura M. Gunsalus, Michael J. Keiser, Katherine S. Pollard:
ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization. 1012841 - Pawel Nalecz-Jawecki, Przemyslaw Szyc, Frederic Grabowski, Marek Kochanczyk, Tomasz Lipniacki:
Information transmission in a cell monolayer: A numerical study. 1012846 - Jonathon Mellor, Maria L. Tang, Emilie Finch, Rachel Christie, Oliver Polhill, Christopher E. Overton, Ann Hoban, Amy Douglas, Sarah R. Deeny, Thomas Ward:
An application of nowcasting methods: Cases of norovirus during the winter 2023/2024 in England. 1012849 - Paul Henriot, Mohamed El-Kassas, Wagida Anwar, Samia A. Girgis, Maha El Gaafary, Kévin Jean, Laura Temime:
An agent-based model to simulate the transmission dynamics of bloodborne pathogens within hospitals. 1012850 - Shunsuke A. Sakai, Ryosuke Nomura, Satoi Nagasawa, Sunggi Chi, Ayako Suzuki, Yutaka Suzuki, Mitsuho Imai, Yoshiaki Nakamura, Takayuki Yoshino, Shumpei Ishikawa, Katsuya Tsuchihara, Shun-Ichiro Kageyama, Riu Yamashita:
SpatialKNifeY (SKNY): Extending from spatial domain to surrounding area to identify microenvironment features with single-cell spatial omics data. 1012854
Volume 21, Number 3, 2025
- Zachary B. Haiman, Alicia Key, Angelo D'alessandro, Bernhard O. Palsson:
RBC-GEM: A genome-scale metabolic model for systems biology of the human red blood cell. 1012109 - Meng Wang, Jonathan Patsenker, Henry Li, Yuval Kluger, Steven H. Kleinstein:
Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction. 1012153 - Simonida Zehr, Sebastian Wolf, Thomas Oellerich, Matthias S. Leisegang, Ralf P. Brandes, Marcel H. Schulz, Timothy Warwick:
GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data. 1012278 - Joseph Masison, Pedro Mendes:
Mathematical modeling reveals ferritin as the strongest cellular driver of dietary iron transfer block in enterocytes. 1012374 - Emma Von Hoene, Amira Roess, Hamdi Kavak, Taylor Anderson:
Synthetic population generation with public health characteristics for spatial agent-based models. 1012439 - Nachshon Korem, Or Duek, Ruonan Jia, Emily Wertheimer, Sierra Metviner, Michael Grubb, Ifat Levy:
Modeling decision-making under uncertainty with qualitative outcomes. 1012440 - Tianai Wang, Christine Quast, Florian Bönner, Malte Kelm, Tobias Zeus, Teresa Lemainque, Ulrich Steinseifer, Michael Neidlin:
Investigation of hemodynamic bulk flow patterns caused by aortic stenosis using a combined 4D Flow MRI-CFD framework. 1012467 - Raheel Asghar, Nan Wu, Noman Ali, Yulei Wang, Mahinur Akkaya:
Computational studies reveal structural characterization and novel families of Puccinia striiformis f. sp. tritici effectors. 1012503 - Larissa M. Oprysk, Maribel Vazquez, Troy Shinbrot:
Internal cohesion gradient as a novel mechanism of collective cell migration. 1012769 - Joseph A. Heng, Michael Woodford, Rafael Polanía:
Efficient numerosity estimation under limited time. 1012790 - Giuseppe de Alteriis, Oliver Sherwood, Alessandro Ciaramella, Robert Leech, Joana Cabral, Federico E. Turkheimer, Paul Expert:
DySCo: A general framework for dynamic functional connectivity. 1012795 - Anna Posfai, Juannan Zhou, David M. McCandlish, Justin B. Kinney:
Gauge fixing for sequence-function relationships. 1012818 - Lilly May, Alice Dauphin, Julijana Gjorgjieva:
Pre-training artificial neural networks with spontaneous retinal activity improves motion prediction in natural scenes. 1012830 - André Victor Ribeiro Amaral, Daniel Wolffram, Paula Moraga, Johannes Bracher:
Post-processing and weighted combination of infectious disease nowcasts. 1012836 - Carla M. Kumbale, Qiang Zhang, Eberhard O. Voit:
Analysis of systemic effects of dioxin on human health through template-and-anchor modeling. 1012840 - Simón Poblete, Mikolaj Mlynarczyk, Marta Szachniuk:
Unknotting RNA: A method to resolve computational artifacts. 1012843 - Elsje J. Burgers, Raju P. Sharma, Carl Joshua S. Eugenio, Muriel M. Heldring, Lukas S. Wijaya, Bob van de Water, Joost B. Beltman:
Computational modelling identifies primary mediators of crosstalk between DNA damage and oxidative stress responses. 1012844 - Callum Gray, Samir Chitnavis, Tamara Buja, Christopher D. P. Duffy:
Predicting the diversity of photosynthetic light-harvesting using thermodynamics and machine learning. 1012845 - Hua Tan, Valer Gotea, Sushil K. Jaiswal, Nancy E. Seidel, David O. Holland, Kevin Fedkenheuer, Abdel G. Elkahloun, Sara R. Bang-Christensen, Laura Elnitski:
iSoMAs: Finding isoform expression and somatic mutation associations in human cancers. 1012847 - Yifan Yao, Scott D. Pauls, Duncan K. Foley, Tomoko Yoshikawa, Sato Honma, Ken-ichi Honma, Ellie McVeigh, Nicolas C. Foley, Rae Silver:
Suprachiasmatic nucleus-wide estimation of oscillatory temporal dynamics. 1012855 - Charlotte Soneson, Lori A. Shepherd, Marcel Ramos, Kevin C. Rue-Albrecht, Johannes Rainer, Hervé Pagès, Vincent J. Carey:
Eleven quick tips for writing a Bioconductor package. 1012856 - Barry Ryan, Riccardo Marioni, T. Ian Simpson:
An integrative network approach for longitudinal stratification in Parkinson's disease. 1012857 - Xinyu Han, Kai Song:
TphPMF: A microbiome data imputation method using hierarchical Bayesian Probabilistic Matrix Factorization. 1012858 - Wei-Yu Lin, Melissa Kartawinata, Bethany R. Jebson, Restuadi Restuadi, Hannah Peckham, Anna Radziszewska, Claire T. Deakin, Coziana Ciurtin, Lucy Wedderburn, Chris Wallace:
Penalised regression improves imputation of cell-type specific expression using RNA-seq data from mixed cell populations compared to domain-specific methods. 1012859 - Julian Heidecke, Jonas Wallin, Peter Fransson, Pratik Singh, Henrik Sjödin, Pascale Claire Stiles, Marina Treskova, Joacim Röcklov:
Uncovering temperature sensitivity of West Nile virus transmission: Novel computational approaches to mosquito-pathogen trait responses. 1012866 - Evangelos Sigalas, Camilo Libedinsky:
Mixed recurrent connectivity in primate prefrontal cortex. 1012867 - Evangelia Vayena, Lea Fuchs, Homa Mohammadi Peyhani, Konrad Lagoda, Bidong D. Nguyen, Wolf-Dietrich Hardt, Vassily Hatzimanikatis:
Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine. 1012869 - Zhengdong Wang, Yifeixue Yang, Ziyi Huang, Wanyun Zhao, Kaiqiang Su, Hengcheng Zhu, Dazhi Yin:
Exploring the transmission of cognitive task information through optimal brain pathways. 1012870 - Guihua Wang, Dan Zhang, Zhifeng He, Bin Mao, Xiao Hu, Li Chen, Qingxin Yang, Zhen Zhou, Yating Zhang, Kepan Linghu, Chao Tang, Zijie Xu, Defu Liu, Junwei Song, Huiying Wang, Yishan Lin, Ruihan Li, Jing-Wen Lin, Lu Chen:
Machine learning-based prediction reveals kinase MAP4K4 regulates neutrophil differentiation through phosphorylating apoptosis-related proteins. 1012877 - Alma Beatrix Stier, Paolo Bonaiuti, János Juhász, Fridolin Gross, Andrea Ciliberto:
lncreased risk of slippage upon disengagement of the mitotic checkpoint. 1012879 - Russell Dinnage, Marian Kleineberg:
Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills. 1012887 - Oliver Eales, Freya M. Shearer, James M. McCaw:
How immunity shapes the long-term dynamics of influenza H3N2. 1012893 - Huu Hoang, Shinichiro Tsutsumi, Masanori Matsuzaki, Masanobu Kano, Keisuke Toyama, Kazuo Kitamura, Mitsuo Kawato:
Predictive reward-prediction errors of climbing fiber inputs integrate modular reinforcement learning with supervised learning. 1012899 - Yang Wu, Ming Chen, Yufang Qin:
Anticancer drug response prediction integrating multi-omics pathway-based difference features and multiple deep learning techniques. 1012905 - Pramod Shinde, Lisa Willemsen, Michael Anderson, Minori Aoki, Saonli Basu, Julie G. Burel, Peng Cheng, Souradipto Ghosh Dastidar, Aidan Dunleavy, Tal Einav, Jamie Forschmiedt, Slim Fourati, Javier Garcia, William Gibson, Jason A. Greenbaum, Leying Guan, Weikang Guan, Jeremy P. Gygi, Brendan Ha, Joe Hou, Jason Hsiao, Yunda Huang, Rick Jansen, Bhargob Kakoty, Zhiyu Kang, James J. Kobie, Mari Kojima, Anna Konstorum, Jiyeun Lee, Sloan A. Lewis, Aixin Li, Eric F. Lock, Jarjapu Mahita, Marcus Mendes, Hailong Meng, Aidan Neher, Somayeh Nili, Lars Rønn Olsen, Shelby Orfield, James A. Overton, Nidhi Pai, Cokie Parker, Brian Qian, Mikkel Rasmussen, Joaquin Reyna, Eve Richardson, Sandra Safo, Josey Sorenson, Aparna Srinivasan, Nicola Thrupp, Rashmi Tippalagama, Raphael Trevizani, Steffen Ventz, Jiuzhou Wang, Cheng-Chang Wu, Ferhat Ay, Barry Grant, Steven H. Kleinstein, Bjoern Peters:
Putting computational models of immunity to the test - An invited challenge to predict B.pertussis vaccination responses. 1012927
Volume 21, Number 4, 2025
- Fillipe Georgiou, Camille Buhl, J. Edward F. Green, Bishnu P. Lamichhane, Ngamta Thamwattana:
Including population and environmental dynamic heterogeneities in continuum models of collective behaviour with applications to locust foraging and group structure. 1011469 - Weixuan Liu, Katherine A. Pratte, Peter J. Castaldi, Craig P. Hersh, Russell P. Bowler, Farnoush Banaei Kashani, Katerina J. Kechris:
A generalized higher-order correlation analysis framework for multi-omics network inference. 1011842 - José A. Carrillo, Hideki Murakawa, Makoto Sato, Miaoxing Wang:
A new paradigm considering multicellular adhesion, repulsion and attraction represent diverse cellular tile patterns. 1011909 - Giulia Moreni, Rares A. Dorcioman, Cyriel M. A. Pennartz, Jorge F. Mejías:
Cell-type-specific firing patterns in a V1 cortical column model depend on feedforward and feedback-driven states. 1012036 - Lana Minier, Jérémy Rouch, Bamdad Sabbagh, Frédéric Bertucci, Eric Parmentier, David Lecchini, Frédéric Sèbe, Nicolas Mathevon, Rémi Emonet:
Visualization and quantification of coral reef soundscapes using CoralSoundExplorer software. 1012050 - Douglas Blackiston, Hannah Dromiack, Caitlin Grasso, Thomas F. Varley, Douglas G. Moore, Krishna Kannan Srinivasan, Olaf Sporns, Josh C. Bongard, Michael Levin, Sara Imari Walker:
Revealing non-trivial information structures in aneural biological tissues via functional connectivity. 1012149 - Sharmilla Chandrasegaran, James P. Sluka, Daryl P. Shanley:
Modelling the spatiotemporal dynamics of senescent cells in wound healing, chronic wounds, and fibrosis. 1012298 - Torbjørn V. Ness, Tom Tetzlaff, Gaute T. Einevoll, David Dahmen:
On the validity of electric brain signal predictions based on population firing rates. 1012303 - Johane Bracamonte, Lionel Watkins, Betty Pat, Louis J. Dell'Italia, Jeffrey J. Saucerman, Jeffrey W. Holmes:
Contributions of mechanical loading and hormonal changes to eccentric hypertrophy during volume overload: A Bayesian analysis using logic-based network models. 1012390 - Xiaoyuan Liu, Jonathan W. Pitchford, George W. A. Constable:
Cell size and selection for stress-induced cell fusion in unicellular eukaryotes. 1012418 - Pascal Mamassian, Vincent de Gardelle:
The confidence-noise confidence-boost (CNCB) model of confidence rating data. 1012451 - Chenyang Gu, Shoji Takada, Giovanni B. Brandani, Tsuyoshi Terakawa:
Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion. 1012493 - Chengze Shen, Eleanor Wedell, Mihai Pop, Tandy J. Warnow:
TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics. 1012593 - Jack Stein, D'artagnan Greene, Flavio H. Fenton, Yohannes Shiferaw:
Mechanism of Arrhythmogenesis Driven by Early After Depolarizations in Cardiac Tissue. 1012635 - Grant Greene, Ian Zonfa, Erzsébet Ravasz Regan:
A Boolean network model of hypoxia, mechanosensing and TGF-β signaling captures the role of phenotypic plasticity and mutations in tumor metastasis. 1012735 - Oliver J. Brady, Leonardo S. Bastos, Jamie M. Caldwell, Simon Cauchemez, Hannah E. Clapham, Illaria Dorigatti, Katy A. M. Gaythorpe, Wenbiao Hu, Laith Hussain-Alkhateeb, Michael A. Johansson, Ahyoung Lim, Velma K. Lopez, Richard James Maude, Jane P. Messina, Erin A. Mordecai, A. Townsend Peterson, Isabel Rodriquez-Barraquer, Ingrid B. Rabe, Diana P. Rojas, Sadie J. Ryan, Henrik Salje, Jan C. Semenza, Quan Minh Tran:
Why the growth of arboviral diseases necessitates a new generation of global risk maps and future projections. 1012771 - Caesar Tawfeeq, Jiyao Wang, Umesh Khaniya, Thomas Madej, James Song, Ravinder Abrol, Philippe Youkharibache:
IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes. 1012813 - Guillermo Pérez Hernández, Peter W. Hildebrand:
mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data. 1012837 - Laia Barjuan, Muhua Zheng, M. Ángeles Serrano:
The multiscale self-similarity of the weighted human brain connectome. 1012848 - Cecilia Fruet, Ella Linxia Müller, Claude Loverdo, Anne-Florence Bitbol:
Spatial structure facilitates evolutionary rescue by drug resistance. 1012861 - Travis Carver Tune, Simon Sponberg:
Nanometer scale difference in myofilament lattice structure of muscle alters muscle function in a spatially explicit model. 1012862 - Gabriele Pozzati, Samuel Coulbourn Flores:
Combining flipped-classroom and spaced-repetition learning in a master-level bioinformatics course. 1012863 - Alexander P. Clark, Mukti Chowkwale, Alexander M. Paap, Stephen Dang, Jeffrey J. Saucerman:
Logic-based modeling of biological networks with Netflux. 1012864 - Benjamin M. Brisard, Kylie D. Cashwell, Stephanie M. Stewart, Logan M. Harrison, Aidan C. Charles, Chelsea V. Dennis, Ivie R. Henslee, Ethan L. Carrow, Heather A. Belcher, Debajit Bhowmick, Paul W. Vos, Maciej Majka, Martin Bier, David M. Hart, Cameron A. Schmidt:
Modeling diffusive search by non-adaptive sperm: Empirical and computational insights. 1012865 - Vincent Hickl, Abid Khan, René M. Rossi, Bruno F. B. Silva, Katharina Maniura-Weber:
Segmentation of dense and multi-species bacterial colonies using models trained on synthetic microscopy images. 1012874 - Suzana de Siqueira Santos, Haixuan Yang, Aldo Galeano, Alberto Paccanaro:
Host centric drug repurposing for viral diseases. 1012876 - Shiwei Fu, Wei Vivian Li:
Predicting and comparing transcription start sites in single cell populations. 1012878 - Nava Leibovich, Sidhartha Goyal:
Limitations and optimizations of cellular lineages tracking. 1012880 - Wenwen Min, Donghai Fang, Jinyu Chen, Shihua Zhang:
SpaMask: Dual masking graph autoencoder with contrastive learning for spatial transcriptomics. 1012881 - Sara Javadzadeh, Aaron Adamson, Jonghun Park, Se-Young Jo, Yuan-Chun Ding, Mehrdad Bakhtiari, Vikas Bansal, Susan L. Neuhausen, Vineet Bafna:
Analysis of targeted and whole genome sequencing of PacBio HiFi reads for a comprehensive genotyping of gene-proximal and phenotype-associated Variable Number Tandem Repeats. 1012885 - Lukás Lochman, Ellen Tanaka Kahiya, Bechara Saade, Tomás Smutný, Jurjen Duintjer Tebbens, Petr Pávek, Veronika Bernhauerová:
Quantifying expression and metabolic activity of genes regulated by pregnane X receptor in primary human hepatocyte spheroids. 1012886 - Rime Diany, Laura K. Fitzgibbon-Collins, Sarah A. Gagliano Taliun:
Ten simple rules for getting started with knowledge mobilization. 1012888 - Timur Olzhabaev, Lukas Müller, Daniel Krause, Dominik Schwudke, Andrew Ernest Torda:
Lipidome visualisation, comparison, and analysis in a vector space. 1012892 - Olivier Gimenez, Andy Royle, Marc Kéry, Chloé R. Nater:
Ten quick tips to get you started with Bayesian statistics. 1012898 - Leo A. Featherstone, Danielle J. Ingle, Wytamma Wirth, Sebastián Duchêne:
How does date-rounding affect phylodynamic inference for public health? 1012900 - Daniel J. B. Clarke, John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Anna I. Byrd, Mano Ram Maurya, Sumana Srinivasan, Keyang Yu, Varduhi Petrosyan, Matthew E. Roth, Miroslav Milinkov, Charles Hadley King, Jeet Kiran Vora, Jonathon Keeney, Christopher Nemarich, William Khan, Alexander Lachmann, Nasheath Ahmed, Alexandra Agris, Juncheng Pan, Srinivasan Ramachandran, Eoin Fahy, Emmanuel Esquivel, Aleksandar Mihajlovic, Bosko Jevtic, Vuk Milinovic, Sean Kim, Patrick McNeely, Tianyi Wang, Eric Wenger, Miguel A. Brown, Alexander Sickler, Yuankun Zhu, Sherry L. Jenkins, Philip D. Blood, Deanne M. Taylor, Adam C. Resnick, Raja Mazumder, Aleksandar Milosavljevic, Shankar Subramaniam, Avi Ma'ayan:
Playbook workflow builder: Interactive construction of bioinformatics workflows. 1012901 - Khanh N. Dinh, Ignacio Vázquez-García, Andrew Chan, Rhea Malhotra, Adam Weiner, Andrew W. McPherson, Simon Tavaré:
CINner: Modeling and simulation of chromosomal instability in cancer at single-cell resolution. 1012902 - Heejin Choi, Chang Hyeong Lee:
The impact of climate change on ecology of tick associated with tick-borne diseases. 1012903 - Zhiyi Zou, Ying Liu, Yuting Bai, Jiawei Luo, Zhaolei Zhang:
scTrans: Sparse attention powers fast and accurate cell type annotation in single-cell RNA-seq data. 1012904 - Logan Wu, Christopher M. Baker, Nicholas Tierney, Kylie Carville, Jodie McVernon, Nick Golding, James M. McCaw, Freya M. Shearer:
Quantifying the impact of contact tracing interview prioritisation strategies on disease transmission: A modelling study. 1012906 - Ruiqi Lyu, Roni Rosenfeld, Bryan Wilder:
Federated epidemic surveillance. 1012907 - Daniela S. Santurio, Luciana R. C. Barros, Ingmar Glauche, Artur C. Fassoni:
Mathematical modeling unveils the timeline of CAR-T cell therapy and macrophage-mediated cytokine release syndrome. 1012908 - Atsushi Matsuda, Mohammad R. K. Mofrad:
Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory. 1012909 - Borana Dollomaja, Huifang E. Wang, Maxime Guye, Julia Makhalova, Fabrice Bartolomei, Viktor K. Jirsa:
Virtual epilepsy patient cohort: Generation and evaluation. 1012911 - Eric R. Schultz, Soren Kyhl, Rebecca Willett, Juan J. de Pablo:
Chromatin structures from integrated AI and polymer physics model. 1012912 - James B. Grotberg, Francesco Romanò, John C. Grotberg:
Flow mechanisms of the air-blood barrier. 1012917 - Yi Cheng, Xingyu Wang, Qiang Zhang, Renkai Ge, Mei Zhou, Yue Dai:
Multiple patterns of persistent inward currents with multiple types of repetitive firings in medullary serotonergic neurons of mice: An experimental and modeling study. 1012918 - Ziyan Jin, Xinyi Zhou, Zhaoyuan Fang:
DelaySSA: stochastic simulation of biochemical systems and gene regulatory networks with or without time delays. 1012919 - Matheus Vitor Ferreira Ferraz, W. Camilla S. Adan, Tayná E. Lima, Adriele J. C. Santos, Sérgio O. de Paula, Rafael Dhalia, Gabriel da Luz Wallau, Rebecca C. Wade, Isabelle F. T. Viana, Roberto D. Lins:
Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning. 1012921 - Alyssa N. Sbarra, Emily Haeuser, Samuel Kidane, Andargie Abate, Ayele M. Abebe, Muktar Ahmed, Alemayehu Tsegaye, Erkihun Amsalu, Aleksandr Y. Aravkin, Akeza A. Asgedom, Nebiyou Bayleyegn, Mulat Dagnew, Biniyam Demisse, Werku Etafa, Getahun Fetensa, Teferi Gebru Gebremeskel, Habtamu Geremew, Abraham T. Gizaw, Gamechu A. Hunde, Hadush N. Meles, Sibhat Migbar, Jason Q. Nguyen, Eshetu Nigussie, Rebecca E. Ramshaw, Sam Rolfe, Biniyam Sahiledengle, Noga Shalev, Yonatan Solomon, Latera Tesfaye, Gesila E. Yesera, Mark Jit, Jonathan F. Mosser:
Fitting dynamic measles models to subnational case notification data from Ethiopia: Methodological challenges and key considerations. 1012922 - Jenny Drnevich, Frederick J. Tan, Fabricio Almeida-Silva, Robert Castelo, Aedín C. Culhane, Sean R. Davis, Maria A. Doyle, Ludwig Geistlinger, Andrew R. Ghazi, Susan P. Holmes, Leo Lahti, Alexandru Mahmoud, Kozo Nishida, Marcel Ramos, Kevin C. Rue-Albrecht, David J. H. Shih, Laurent Gatto, Charlotte Soneson:
Learning and teaching biological data science in the Bioconductor community. 1012925 - Sorenza P. Bastiaens, Davide Momi, John D. Griffiths:
A comprehensive investigation of intracortical and corticothalamic models of the alpha rhythm. 1012926 - Hanah Goetz, Rong Zhang, Xiao Wang, Xiao-Jun Tian:
Resource competition-driven bistability and stochastic switching amplify gene expression noise. 1012931 - Toma M. Marinov, Perry T. Wasdin, Gwen Jordaan, Alexis K. Janke, Alexandra A. Abu-Shmais, Ivelin S. Georgiev:
An expandable synthetic library of human paired antibody sequences. 1012932 - Gabriel Matías Lorenz, Nicola Marie Engel, Marco Celotto, Loren Koçillari, Sebastiano Curreli, Tommaso Fellin, Stefano Panzeri:
MINT: A toolbox for the analysis of multivariate neural information coding and transmission. 1012934 - Yufei Wu, Morgan A. Benson, Sean X. Sun:
Fluid and solute transport by cells and a model of systemic circulation. 1012935 - Ana Laura Granados-Tristán, Mauricio Carrillo-Tripp, Carlos Eduardo Hernández-Luna, Aldo Herrera-Rodulfo, Laura Adiene González-Escalante, Ana Leticia Arriaga-Guerrero, Beatriz Silva-Ramírez, Brenda Leticia Escobedo-Guajardo, Roberto Mercado-Hernández, Mario Bermúdez de León, Katia Peñuelas-Urquides:
Mycobacterium susceptibility to ivermectin by inhibition of eccD3, an ESX-3 secretion system component. 1012936 - David N. White, Johannes Burge:
How distinct sources of nuisance variability in natural images and scenes limit human stereopsis. 1012945 - Davide Chicco, Vasco Coelho:
A teaching proposal for a short course on biomedical data science. 1012946 - Troy J. Kieran, Taronna R. Maines, Jessica A. Belser:
Eleven quick tips to unlock the power of in vivo data science. 1012947 - Wenqian Tu, Lihua Zhang:
Integrating multiple spatial transcriptomics data using community-enhanced graph contrastive learning. 1012948 - David J. Pascall, Christopher Jackson, Stephanie Evans, Theodore Gouliouris, Christopher J. R. Illingworth, Stefan G. Piatek, Julie V. Robotham, Oliver Stirrup, Ben Warne, Judith Breuer, Daniela De Angelis:
The NOSTRA model: Coherent estimation of infection sources in the case of possible nosocomial transmission. 1012949 - Christopher J. Whyte, Eli J. Müller, Jaan Aru, Matthew E. Larkum, Yohan John, Brandon R. Munn, James M. Shine:
A burst-dependent thalamocortical substrate for perceptual awareness. 1012951 - Jiaxin Hu, Jesse N. Weber, Lauren E. Fuess, Natalie C. Steinel, Daniel I. Bolnick, Miaoyan Wang:
A spectral framework to map QTLs affecting joint differential networks of gene co-expression. 1012953 - Jay S. Coggan, Polina Shichkova, Henry Markram, Daniel X. Keller:
Seizure and redox rescue in a model of glucose transport deficiency. 1012959 - Emma B. Hodcroft, Martin Wohlfender, Richard A. Neher, Julien Riou, Christian L. Althaus:
Estimating Re and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2. 1012960 - Yuanxi Li, Bing Zhang, Jinqi Liu, Rubin Wang:
Neural energy coding patterns of dopaminergic neural microcircuit and its impairment in major depressive disorder: A computational study. 1012961 - Alexander M. Morin, Eric Ching-Pan Chu, Paul Pavlidis:
Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics. 1012962 - Caiyu Zhang, Chenyu Liu, Zhuoru Wang, Di Wang, Wenli Chen, Jian Li, Qianyi Lu, Jiajun Zhou, Yetong Chang, Peng Wang, Yue Gao, Junwei Wang, Hui Zhi, Shangwei Ning:
Comprehensive characterization of respiratory genes based on a computational framework in pan-cancer to develop stratified treatment strategies. 1012963 - Yee Chuen Teoh, Mohammed Sakib Noor, Sina Aghakhani, Jack Girton, Guiping Hu, Ratul Chowdhury:
Viral escape-inspired framework for structure-guided dual bait protein biosensor design. 1012964 - Sander W. Keemink, Mark C. W. van Rossum:
Biases in neural population codes with a few active neurons. 1012969 - Zachary Mobille, Usama Bin Sikandar, Simon Sponberg, Hannah Choi:
Temporal resolution of spike coding in feedforward networks with signal convergence and divergence. 1012971 - Mihriban Seyis, Zahra Razaghi-Moghadam, Zoran Nikoloski:
Flux-sum coupling analysis of metabolic network models. 1012972 - Raphaël Bergoin, Alessandro Torcini, Gustavo Deco, Mathias Quoy, Gorka Zamora-López:
Emergence and maintenance of modularity in neural networks with Hebbian and anti-Hebbian inhibitory STDP. 1012973 - Ihab Hashem, Jian Wang, Jan F. M. Van Impe:
A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes. 1012974 - Sarit Felicia Anais Szpiro, Charlie S. Burlingham, Eero P. Simoncelli, Marisa Carrasco:
Perceptual learning improves discrimination but does not reduce distortions in appearance. 1012980 - Alexandre Blanc, François Laurent, Alex Barbier-Chebbah, Hugues Van Assel, Benjamin T. Cocanougher, Benjamin M. W. Jones, Peter Hague, Marta Zlatic, Rayan Chikhi, Christian L. Vestergaard, Tihana Jovanic, Jean-Baptiste Masson, Chloé Barré:
Statistical signature of subtle behavioral changes in large-scale assays. 1012990 - Yoshitaka Kimori:
RMPJ: An ImageJ plugin for morphological information processing in biomedical images. 1012992 - Jin Ke, Hayoung Song, Zihan Bai, Monica D. Rosenberg, Yuan Chang Leong:
Dynamic brain connectivity predicts emotional arousal during naturalistic movie-watching. 1012994 - Ian Roberts, Richard G. Everitt, Jere Koskela, Xavier Didelot:
Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model. 1012995 - Wasim Abbas, Sieun Lee, Sangil Kim:
Joint estimation of hand-foot-mouth disease model and prediction in korea using the ensemble kalman filter. 1012996 - Archana Prabahar, Connie S. Chamberlain, Ray Vanderby, William L. Murphy, William Dangelo, Kulkarni Mangesh, Bryan Brown, Barsanjit Mazumder, Stephen Badylak, Peng Jiang:
Transcriptomic landscape around wound bed defines regenerative versus non-regenerative outcomes in mouse digit amputation. 1012997 - Editorial Note: In silico knockout studies of xenophagic capturing of Salmonella. 1012998
- Mona Nourbakhsh, Yuanning Zheng, Humaira Noor, Hongjin Chen, Subhayan Akhuli, Matteo Tiberti, Olivier Gevaert, Elena Papaleo:
Revealing cancer driver genes through integrative transcriptomic and epigenomic analyses with Moonlight. 1012999 - Editorial Note: Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis. 1013003
- Wei He, Xu Tian, Xue Li, Peifu Han, Shuang Wang, Lin Liu, Tao Song:
TGF-M: Topology-augmented geometric features enhance molecular property prediction. 1013004 - Laetitia Grabot, Garance Merholz, Jonathan Winawer, David J. Heeger, Laura Dugué:
Traveling waves in the human visual cortex: An MEG-EEG model-based approach. 1013007 - Yannick Jadoul, Taylor A. Hersh, Elias Fernández Domingos, Marco Gamba, Livio Favaro, Andrea Ravignani:
An evolutionary model of rhythmic accelerando in animal vocal signalling. 1013011 - Expression of Concern: HiSV: A control-free method for structural variation detection from Hi-C data. 1013016
- Tim Vriens, Eliana Vassena, Giovanni Pezzulo, Gianluca Baldassarre, Massimo Silvetti:
Meta-Reinforcement Learning reconciles surprise, value, and control in the anterior cingulate cortex. 1013025 - Jacob N. Stapley, Jonathan I. D. Hamley, María-Gloria Basáñez, Martin Walker:
Modelling transmission thresholds and hypoendemic stability for onchocerciasis elimination. 1013026 - Claire Lugrin, Jie Hu, Christian C. Ruff:
A computational account of multiple motives guiding context-dependent prosocial behavior. 1013032 - Wen-Wei Shao, Qi Shao, Hai-Huan Xu, Guan-Ji Qiao, Run-Xuan Wang, Zhi-Yun Ma, Wei-Wei Meng, Zhuo-Bin Yang, Yun-Liang Zang, Xiao-Hong Li:
Repetitive training enhances the pattern recognition capability of cultured neural networks. 1013043 - Romain Brette:
Theory of axo-axonic inhibition. 1013047
Volume 21, Number 5, 2025
- Quintin Pope, Rohan Varma, Christine A. Tataru, Maude M. David, Xiaoli Z. Fern:
Learning a deep language model for microbiomes: The power of large scale unlabeled microbiome data. 1011353 - Peter Methys Degen, Matús Medo:
Replicability of bulk RNA-Seq differential expression and enrichment analysis results for small cohort sizes. 1011630 - Miriam Schnitzerlein, Eric Greto, Anja Wegner, Anna Möller, Oliver Aust, Oumaima B. Brahim, David B. Blumenthal, Vasily Zaburdaev, Stefan Uderhardt:
Cellular morphodynamics as quantifiers for functional states of resident tissue macrophages in vivo. 1011859 - Anastasia Galperina, Gabriele Andrea Lugli, Christian Milani, Willem M. De Vos, Marco Ventura, Anne Salonen, Bonnie L. Hurwitz, Alise J. Ponsero:
The Aggregated Gut Viral Catalogue (AVrC): A unified resource for exploring the viral diversity of the human gut. 1012268 - Miriam Goldman, Chunyu Zhao, Katherine S. Pollard:
Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM). 1012277 - Yuru Song, Marcus K. Benna:
Parallel synapses with transmission nonlinearities enhance neuronal classification capacity. 1012285 - Naruemon Rueangkham, Miguel Valle-Inclán Cabello, Franziska Lautenschläger, Rhoda J. Hawkins:
Nuclear deformation by microtubule molecular motors. 1012305 - Sarafa A. Iyaniwura, Tyler Cassidy, Ruy M. Ribeiro, Alan S. Perelson:
A multiscale model of the action of a capsid assembly modulator for the treatment of chronic hepatitis B. 1012322 - Romani Osbourne, Kelly M. Thayer:
Structural and mechanistic diversity in p53-mediated regulation of organismal longevity across taxonomical orders. 1012382 - Anna Zhukova, Olivier Gascuel:
Accounting for contact tracing in epidemiological birth-death models. 1012461 - Wenjun Zhao, Erica Larschan, Björn Sandstede, Ritambhara Singh:
Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation. 1012476 - Yanchao Li, Quan Zou, Qi Dai, Antony Stalin, Ximei Luo:
Identifying the DNA methylation preference of transcription factors using ProtBERT and SVM. 1012513 - Borjan Milinkovic, Lionel C. Barnett, Olivia Carter, Anil K. Seth, Thomas Andrillon:
Capturing the emergent dynamical structure in biophysical neural models. 1012572 - Luis de la Cuesta-Ferrer, Christina Koß, Sarah Starosta, Nils Kasties, Daniel Lengersdorf, Frank Jäkel, Maik C. Stüttgen:
Stimulus uncertainty and relative reward rates determine adaptive responding in perceptual decision-making. 1012636 - Di Wu, Qi Ouyang, Hongli Wang, Youdong Mao:
A kinetic model for USP14 regulated substrate degradation in 26S proteasome. 1012761 - Lion Schulz, Yannick Streicher, Eric Schulz, Rahul Bhui, Peter Dayan:
Mechanisms of mistrust: A Bayesian account of misinformation learning. 1012814 - Daniel Schmid, Heiko Neumann:
A model of thalamo-cortical interaction for incremental binding in mental contour-tracing. 1012835 - Lenka Kopfová, Josef Tkadlec:
Colonization times in Moran process on graphs. 1012868 - Fenglian Pan, You Zhou, Carolina Vivas-Valencia, Nan Kong, Carol Ott, Mohammad S. Jalali, Jian Liu:
Modeling opioid overdose events recurrence with a covariate-adjusted triggering point process. 1012889 - Joshua T. S. Hewson, Alana Jaskir, Michael J. Frank:
Many roads to minimizing regret: A comparison of Wang et al (2024) and OpAL* models of adaptive striatal dopamine. 1012920 - Leo D'Amato, Gian Luca Lancia, Giovanni Pezzulo:
The geometry of efficient codes: How rate-distortion trade-offs distort the latent representations of generative models. 1012952 - Catalina M. Medina, Julia A. Palacios, Volodymyr M. Minin:
Accounting for reporting delays in real-time phylodynamic analyses with preferential sampling. 1012970 - Jaspreet Pannu, Doni Bloomfield, Robert MacKnight, Moritz S. Hanke, Alex Zhu, Gabe Gomes, Anita Cicero, Thomas V. Inglesby:
Dual-use capabilities of concern of biological AI models. 1012975 - Zhuolin Qu, Denis D. Patterson, Lihong Zhao, Joan Ponce, Christina Edholm, Olivia F. Prosper, Lauren M. Childs:
Mathematical modeling of malaria vaccination with seasonality and immune feedback. 1012988 - Zoë Lange, Franziska Matthäus, Mingfeng Qiu:
Vertex models capturing subcellular scales in epithelial tissues. 1012993 - Mukun Chen, Jia Wu, Shirui Pan, Fu Lin, Bo Du, Xiuwen Gong, Wenbin Hu:
Knowledge-aware contrastive heterogeneous molecular graph learning. 1013008 - Dieter Vanderelst, Herbert Peremans:
How swarming bats can use the collective soundscape for obstacle avoidance. 1013013 - Joseph James Tharayil, Jorge Blanco Alonso, Silvia Farcito, Bryn A. Lloyd, Armando Romani, Elvis Boci, Antonino Cassara, Felix Schürmann, Esra Neufeld, Niels Kuster, Michael Reimann:
BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models. 1013023 - Fabricio Cravo, Gayathri Prakash, Matthias Függer, Thomas Nowak:
MobsPy: A programming language for biochemical reaction networks. 1013024 - Chenchen Jia, Hai-Yun Wang, Jianping Zhao, Junfeng Xia, Chun-Hou Zheng:
scSDNE: A semi-supervised method for inferring cell-cell interactions based on graph embedding. 1013027 - Péter Polcz, István Z. Reguly, Kálmán Tornai, János Juhász, Sándor Pongor, Attila Csikász-Nagy, Gábor Szederkényi:
Smart epidemic control: A hybrid model blending ODEs and agent-based simulations for optimal, real-world intervention planning. 1013028 - Elvis A. F. Martis, Stéphane Téletchéa:
Ten quick tips to perform meaningful and reproducible molecular docking calculations. 1013030 - Neda Shahidi, Fernando Rozenblit, Mohammad H. Khani, Helene M. Schreyer, Matthias Mietsch, Dario A. Protti, Tim Gollisch:
Filter-based models of suppression in retinal ganglion cells: Comparison and generalization across species and stimuli. 1013031 - Kathryn C. Krupinsky, Christian T. Michael, Pariksheet Nanda, Joshua T. Mattila, Denise E. Kirschner:
Distinguishing multiple roles of T cell and macrophage involvement in determining lymph node fates during Mycobacterium tuberculosis infection. 1013033 - Xiaoxiao Cheng, Shixian Shen, Ekaterina Ivanova, Gerolamo Carboni, Atsushi Takagi, Etienne Burdet:
Human impedance modulation to improve visuo-haptic perception. 1013042 - William R. Shoemaker, Álvaro Sánchez, Jacopo Grilli:
Macroecological patterns in experimental microbial communities. 1013044 - William Gilpin:
Optimization hardness constrains ecological transients. 1013051 - Arpit C. Swain, José A. M. Borghans, Rob J. De Boer:
How are estimated cellular turnover rates influenced by the dynamics of a source population? 1013052 - Rotem Botvinik-Nezer, Stephan Geuter, Martin A. Lindquist, Tor D. Wager:
Expectation generation and its effect on subsequent pain and visual perception. 1013053 - Sneha Aenugu, John P. O'doherty:
Building momentum: A computational account of persistence toward long-term goals. 1013054 - Katharina Waury, Stefan Lelieveld, Sanne Abeln, Henk-Jan van den Ham:
Comparison of sequence- and structure-based antibody clustering approaches on simulated repertoire sequencing data. 1013057 - Yanbo Lian, Anthony N. Burkitt:
Relating sparse and predictive coding to divisive normalization. 1013059 - Tong Liu, Zihuan Liu, Wenke Sun, Adeethyia Shankar, Yongzhong Zhao, Xiaodi Wang:
M-band wavelet-based multi-view clustering of cells. 1013060 - Zahra Vahdat, Oliver Gambrell, Jonas Fisch, Eckhard Friauf, Abhyudai Singh:
Inferring synaptic transmission from the stochastic dynamics of the quantal content: An analytical approach. 1013067 - Sofia Farina, Alessandro Cattabiani, Darshan Mandge, Polina Shichkova, James B. Isbister, Jean Jacquemier, James Gonzalo King, Henry Markram, Daniel X. Keller:
A multiscale electro-metabolic model of a rat neocortical circuit reveals the impact of ageing on central cortical layers. 1013070 - Owen M. O'Connor, Mary J. Dunlop:
Cell-TRACTR: A transformer-based model for end-to-end segmentation and tracking of cells. 1013071 - Qi Deng, Woldegebriel Assefa Woldegerima, Wenjing Zhang, Ali Asgary, Jude Dzevela Kong, Sarah Flicker, Nicholas H. Ogden, James Orbinski, Nicola Luigi Bragazzi, Jianhong Wu:
Uncovering the impact of infection routes on within-host MPXV dynamics: Insights from a mathematical modeling study. 1013073 - Debby Dan Wang, Yuting Huang:
Scoring protein-ligand binding structures through learning atomic graphs with inter-molecular adjacency. 1013074 - Sebastian Höpfl, Merih Özverin, Helena Nowack, Raluca Tamas, Andrew G. Clark, Nicole Radde, Monilola A. Olayioye:
Integrated mathematical and experimental modeling uncovers enhanced EMT plasticity upon loss of the DLC1 tumor suppressor. 1013076 - Lucie Riglet, Catherine Quilliet, Christophe Godin, Karin John, Isabelle Fobis-Loisy:
Geometric and mechanical guidance: Role of stigmatic epidermis in early pollen tube pathfinding in arabidopsis. 1013077 - Raffaele Marchesi, Nicolo Micheletti, Nicholas I-Hsien Kuo, Sebastiano Barbieri, Giuseppe Jurman, Venet Osmani:
Generative AI mitigates representation bias and improves model fairness through synthetic health data. 1013080 - Zeyuan Ye, Haoran Li, Liang Tian, Changsong Zhou:
The effects of the post-delay epochs on working memory error reduction. 1013083 - Kaushik N. Shankar, Talid Sinno, Scott L. Diamond:
Multiscale simulations that incorporate patient-specific neural network models of platelet calcium signaling predict diverse thrombotic outcomes under flow. 1013085 - Malthe Brændholt, Niia Nikolova, Melina Vejlø, Leah Banellis, Francesca Fardo, Daniel S. Kluger, Micah Allen:
The respiratory cycle modulates distinct dynamics of affective and perceptual decision-making. 1013086 - Yukako Yamane, Yuzhe Li, Keita Matsumoto, Ryota Kanai, Miles Desforges, Carlos Enrique Gutierrez, Kenji Doya:
Optical Neuroimage Studio (OptiNiSt): Intuitive, scalable, extendable framework for optical neuroimage data analysis. 1013087 - Teresa W. Lo, Kevin J. Cutler, H. James Choi, Paul A. Wiggins:
OmniSegger: A time-lapse image analysis pipeline for bacterial cells. 1013088 - Jan Babic, Tjasa Kunavar, Erhan Oztop, Mitsuo Kawato:
Success-efficient/failure-safe strategy for hierarchical reinforcement motor learning. 1013089 - Dori M. Grijseels, M. Banqueri, Keerthana Iyer, Lee Hanlin, Melanie Ortiz Alvarez de la Campa, David Pagliaccio, Bittu K. Rajaraman, Eitan Schechtman:
Ten simple rules for queer data collection and analysis by STEM researchers. 1013091 - Ori Hendler, Ronen Segev, Maoz Shamir:
Noise correlations and neuronal diversity may limit the utility of winner-take-all readout in a pop out visual search task. 1013092 - Maria Inmaculada Villanueva, Anna Pellisé-Tintoré, María Pérez-Rodríguez, Laura Nogué, Pooja Vaziraani, Iris Soveral, Fátima Crispi, Olga Gómez, Patricia Garcia-Cañadilla, Oscar Camara, Bart Bijnens, Gabriel Bernardino:
Understanding the hemodynamic changes in fetuses with coarctation of the aorta using a lumped model of fetal circulation. 1013096 - Alberto Portela, Julio R. Banga, Marcos Matabuena:
Conformal prediction for uncertainty quantification in dynamic biological systems. 1013098 - Florian A. Overberg, Narges Jamshidi Khameneh, Timothy Krüger, Markus Engstler, Gerhard Gompper, Dmitry A. Fedosov:
Modelling motility of Trypanosoma brucei. 1013111 - Yuxiang Zhan, Francesco Musella, Frank Alber:
MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures. 1013114 - Cheng Xing, Ronald Xie, Gary D. Bader:
RETINA: Reconstruction-based pre-trained enhanced TransUNet for electron microscopy segmentation on the CEM500K dataset. 1013115 - Elnaz Nemati, David B. Grayden, Anthony N. Burkitt, Parvin Zarei Eskikand:
Balancing prior knowledge and sensory data in a predictive coding model of coherent motion detection. 1013116 - Cesar Celis Ceballos, Nourdin Chadly, Eric Lowet, Rodrigo F. O. Pena:
Interleaved single and bursting spiking resonance in neurons. 1013126
Volume 21, Number 6, 2025
- Jingming Xue, Robert C. Wilson, Mary A. Peterson:
Semantic influences on object detection: Drift diffusion modeling provides insights regarding mechanism. 1012269 - Hilson G. Vilar de Andrade, Élisson da Silva Rocha, Kayo H. de Carvalho Monteiro, Cleber Matos de Morais, Danielle Christine Moura dos Santos, Dimas Cassimiro Nascimento, Raphael A. Dourado, Theo Lynn, Patricia Takako Endo:
On the usage of artificial intelligence in leprosy care: A systematic literature review. 1012550 - Nicholas A. Rondoni, Fan Lu, Daniel B. Turner-Evans, Marcella Gomez:
Predicting neuronal firing from calcium imaging using a control theoretic approach. 1012603 - Stephen Catterall, Thibaud Porphyre, Glenn Marion:
iPAR: A framework for modelling and inferring information about disease spread when the populations at risk are unknown. 1012622 - Hannah Waddel, Katia Koelle, Max S. Y. Lau:
ScITree: Scalable Bayesian inference of transmission tree from epidemiological and genomic data. 1012657 - Giulio Filippi, James C. Knight, Andrew Philippides, Paul Graham:
Lateralised memory networks may explain the use of higher-order visual features in navigating insects. 1012670 - Ada W. C. Yan, Ildar Sadreev, Jonas Mackerodt, Yan Zhang, Derek C. Macallan, Robert Busch, Becca Asquith:
The impact of model assumptions in interpreting cell kinetic studies. 1012704 - Qile Yang, Ksenia R. Safina, Kieu Diem Quynh Nguyen, Zewen K. Tuong, Nicholas Borcherding:
scRepertoire 2: Enhanced and efficient toolkit for single-cell immune profiling. 1012760 - Wentao Ma, Chunwu Yu:
From experimental clues to theoretical modeling: Evolution associated with the membrane-takeover at an early stage of life. 1012763 - Zichao Liu, Yinyun Li:
Investigate channel rectifications and neural dynamics by an electrodiffusive Gauss-Nernst-Planck approach. 1012883 - Hakim Benkirane, Maria Vakalopoulou, David Planchard, Julien Adam, Ken Olaussen, Stefan Michiels, Paul-Henry Cournède:
Multimodal CustOmics: A unified and interpretable multi-task deep learning framework for multimodal integrative data analysis in oncology. 1013012 - Zhanhao Zhang, Iryna Zabaikina, César Nieto, Zahra Vahdat, Pavol Bokes, Abhyudai Singh:
Stochastic gene expression in proliferating cells: Differing noise intensity in single-cell and population perspectives. 1013014 - William R. Cannon, Ethan King, Katherine A. Huening, Justin A. North:
Redox poise in R. rubrum phototrophic growth drives large-scale changes in macromolecular pathways. 1013015 - Jana Masselink, Markus Lappe:
Adaptation across the 2D population code explains the spatially distributive nature of motor learning. 1013041 - Janis Keck, Caswell Barry, Christian F. Doeller, Jürgen Jost:
Impact of symmetry in local learning rules on predictive neural representations and generalization in spatial navigation. 1013056 - Mélodie Ambroset, Marie Anselmet, Benedetti Clément, Arthur Meslin, Aurelien Maillot, Rouvière Christian, Maucort Guillaume, Marine Breuilly, Albert Marvin, Gaëlle Letort, Antonio Trullo, Volker Bäcker, Jerome Mutterer, Fabrice Cordelières, Thierry Pécot, Minh Son Phan, Stéphane Rigaud, Magalie Feyeux, Perrine Paul-Gilloteaux, Anne-Sophie Macé, Jean-Yves Tinevez:
F-BIAS: Towards a distributed national core facility for bioimage analysis †. 1013058 - Rosie Berners-Lee, Eamonn Gilmore, Francisco Berkemeier, Michael A. Boemo:
Regulation of replication timing in Saccharomyces cerevisiae. 1013066 - Yujia Wen, Zhixue He, Chen Shen, Jun Tanimoto:
Indirect punishment can outperform direct punishment in promoting cooperation in structured populations. 1013068 - Pawel Górecki, Alexey Markin, Sriram Vijendran, Oliver Eulenstein:
Computing generalized cophenetic distances under all Lp norms: A near-linear time algorithmic framework. 1013069 - Siyu Chen, Sudhir Venkatesan, Sofie Arnetorp, Klas Bergenheim, Sabada Dube, Wilhelmine Meeraus, Cátia Ferreira, Sylvia Taylor, Lisa J. White:
Features influencing the health and economic impact of preventing COVID-19 in immunocompromised individuals. 1013072 - Ryan J. Rowekamp, Tatyana O. Sharpee:
Computations that sustain neural feature selectivity across processing stages. 1013075 - Adithan Kandasamy, Yi-Ting Yeh, Ricardo Serrano, Mark Mercola, Juan C. del Álamo:
Uncertainty-aware traction force microscopy. 1013079 - Richard Pang:
Balanced state of networks of winner-take-all units. 1013081 - Caroline I. Larkin, Matthew D. Dunn, Jason E. Shoemaker, William B. Klimstra, James R. Faeder:
A detailed kinetic model of Eastern equine encephalitis virus replication in a susceptible host cell. 1013082 - Ehsan Sabri, Renata Batista-Brito:
Isolating single cycles of neural oscillations in population spiking. 1013084 - Xuexin Yu, Jing Hu, Yuhao Tan, Mingyao Pan, Hongyi Zhang, Bo Li:
MitoTracer facilitates the identification of informative mitochondrial mutations for precise lineage reconstruction. 1013090 - Michael Satchell, Edith Butel-Fry, Zahraa Noureddine, Alexis Simmons, Nicolette Ognjanovski, Sara J. Aton, Michal R. Zochowski:
Cholinergic modulation of neural networks supports sequential and complementary roles for NREM and REM states in memory consolidation. 1013097 - Emre Baspinar, Martina Simonti, Hadi Srour, Mathieu Desroches, Daniele Avitabile, Massimo Mantegazza:
GABAergic neurons can facilitate the propagation of cortical spreading depolarization: experiments in mouse neocortical slices and a novel neural field computational model. 1013099 - Daiki Wakita, Yuriko Sobu, Naoko Kaneko, Takeshi Kano:
A mathematical model suggests collectivity and inconstancy enhance the efficiency of neuronal migration in the adult brain. 1013105 - Satya Spandana Boddu, K. Michael Martini, Ilya Nemenman, Nic M. Vega:
Variance in C. elegans gut bacterial load suggests complex host-microbe dynamics. 1013110 - Mingfang Zhang, Raluca Chitic, Sander M. Bohté:
Energy optimization induces predictive-coding properties in a multi-compartment spiking neural network model. 1013112 - Katherine Owens, Aminur Rahman, Ivana Bozic:
Spatiotemporal dynamics of tumor-CAR T-cell interaction following local administration in solid cancers. 1013117 - Jessie Rademacher, Tineke Grent-'t-Jong, Davide Rivolta, Andreas Sauer, Bertram Scheller, Guillermo Gonzalez-Burgos, Christoph Metzner, Peter J. Uhlhaas:
Computational modeling of ketamine-induced changes in gamma-band oscillations: The contribution of parvalbumin and somatostatin interneurons. 1013118 - Carlos Alberto Gomez-Uribe, Japheth Gado, Meiirbek Islamov:
Designing diverse and high-performance proteins with a large language model in the loop. 1013119 - Swathi Anil, Dan F. M. Goodman, Marcus Ghosh:
Fusing multisensory signals across channels and time. 1013125 - Priyan Bhattacharya, Alban Linnenbach, Andrew P. South, Ubaldo Martinez-Outschoorn, Joseph M. Curry, Jennifer M. Johnson, Larry A. Harshyne, My G. Mahoney, Adam J. Luginbuhl, Rajanikanth Vadigepalli:
Tumor microenvironment governs the prognostic landscape of immunotherapy for head and neck squamous cell carcinoma: A computational model-guided analysis. 1013127 - Kevin J. Flynn, Andrew Y. Morozov:
Resource acquisition in diel cycles and the cost of growing quickly. 1013132 - Jiawei Huang, Yuxuan Du, Kevin R. Kelly, Jinchi Lv, Yingying Fan, Jiang F. Zhong, Fengzhu Sun:
DeepDeconUQ estimates malignant cell fraction prediction intervals in bulk RNA-seq tissue. 1013133 - Lindsay S. Anderson, Jamie D. Costabile, Sina Schwinn, Delia Calderon, Martin Haesemeyer:
Sensorimotor integration enhances temperature stimulus processing. 1013134 - Ximena León Du'mottuchi, Nicole Creanza:
The role of learned song in the evolution and speciation of Eastern and Spotted towhees. 1013135 - Qi Sun, Ling-Hao Xu, Alan A. Stocker:
A linear perception-action mapping accounts for response range-dependent biases in heading estimation from optic flow. 1013147 - Ismael Jaras, Marcos E. Orchard, Pedro Maldonado, Rodrigo C. Vergara:
Unveiling the role of local metabolic constraints on the structure and activity of spiking neural networks. 1013148 - Karoline Horgmo Jæger, Aslak Tveito:
Electrodiffusion dynamics in the cardiomyocyte dyad at nano-scale resolution using the Poisson-Nernst-Planck (PNP) equations. 1013149 - Wiep Stikvoort, Eider Pérez-Ordoyo, Iván Mindlin, Anira Escrichs, Jacobo D. Sitt, Morten L. Kringelbach, Gustavo Deco, Yonatan Sanz Perl:
Nonequilibrium brain dynamics elicited as the origin of perturbative complexity. 1013150 - Roland M. Dries, Kim Y. Renders, Jaap A. Kaandorp:
Studying gastrulation by invagination: The bending of a cell sheet by mechanical cell properties using 3D deformable cell based simulations. 1013151 - Christine M. Lim, Michele Vendruscolo:
Proteostasis signatures in human diseases. 1013155 - Alexandra M. Campbell, Anna C. Kula, Rachel S. Jabaily, Brad Oberle, Brian Sidoti, Alex Capaldi, Erin N. Bodine:
Predicting potential recovery of the endangered bromeliad Tillandsia utriculata: An agent-based modeling approach. 1013157 - Elisa Domínguez-Hüttinger, Eliezer Flores-Garza, José Luis Caldú-Primo, Harley Day, Abihail Roque Ramírez, Reiko J. Tanaka:
History-dependent switch-like differentiation of keratinocytes in response to skin barrier damage. 1013162 - Chrysovalantis Voutouri, Lance L. Munn, Triantafyllos Stylianopoulos, Rakesh K. Jain:
Biomarkers of mRNA vaccine efficacy derived from mechanistic modeling of tumor-immune interactions. 1013163 - Kaylee Beine, Lauric Feugere, Alexander Turner, Katharina C. Wollenberg Valero:
Network architecture of transcriptomic stress responses in zebrafish embryos. 1013164 - Lilach Schneor, Dafna Tussia-Cohen, Evgeny Fraimovitch, Sivan Friedman, Tzachi Hagai:
Evolutionary divergence of induced versus constitutive antiviral gene expression levels between primates and rodents. 1013165 - Correction: Including population and environmental dynamic heterogeneities in continuum models of collective behaviour with applications to locust foraging and group structure. 1013167
- Mihkel Saluri, Michael Landreh, Patrick Bryant:
AI-first structural identification of pathogenic protein target interfaces. 1013168 - Nuray Sogunmez Erdogan, Deniz Eroglu:
Sparse deconvolution of cell type medleys in spatial transcriptomics. 1013169 - Sonia T. Gazeau, Xiaoyan Deng, Elsa Brunet-Ratnasingham, Daniel E. Kaufmann, Catherine Larochelle, Penelope A. Morel, Jane M. Heffernan, Courtney L. Davis, Amber M. Smith, Adrianne L. Jenner, Morgan Craig:
Using virtual patient cohorts to uncover immune response differences in cancer and immunosuppressed COVID-19 patients. 1013170 - Peng Zhao, Boyang Wang, Yi Rong, Ye Yuan, Jian Liu, Hong Huo, Zhuyong Liu, Zhaoyu Li, Tao Fang:
The roles of feedback loops in the Caenorhabditis elegans rhythmic forward locomotion. 1013171 - Torkel E. Loman, Yingbo Ma, Vasily Ilin, Shashi Gowda, Niklas Korsbo, Nikhil Yewale, Chris Rackauckas, Samuel A. Isaacson:
Correction: Catalyst: Fast and flexible modeling of reaction networks. 1013175 - Arun S. Mahadevan, Byron L. Long, Chenyue W. Hu, David T. Ryan, Nicolas E. Grandel, George L. Britton, Marisol Bustos, Maria A. Gonzalez Porras, Katerina Stojkova, Andrew Ligeralde, Hyeonwi Son, John Shannonhouse, Jacob T. Robinson, Aryeh Warmflash, Eric M. Brey, Yu Shin Kim, Amina A. Qutub:
Correction: cytoNet: Spatiotemporal network analysis of cell communities. 1013176 - Nao Yamamoto, Daniel T. Citron, Samuel M. Mwalili, Duncan Kioi Gathungu, Diego F. Cuadros, Anna Bershteyn:
Uncovering the impact of randomness in HIV hotspot formation: A mathematical modeling study. 1013178 - Matteo Priorelli, Ivilin Peev Stoianov, Giovanni Pezzulo:
Embodied decisions as active inference. 1013180 - Ian Syndergaard, Daniel B. Free, Dario Farina, Steven K. Charles:
Feedback parameters for a closed-loop multiple-input multiple-output model of the upper limb. 1013183 - Matthew R. Baker, Bryan T. Klassen, Michael A. Jensen, Gabriela Ojeda Valencia, Hossein Heydari, Nuri F. Ince, Klaus-Robert Müller, Kai J. Miller:
Parameterization of intraoperative human microelectrode recordings: Linking action potential morphology to brain anatomy. 1013184 - Samuel Eriksson Lidbrink, Rebecca J. Howard, Nandan Haloi, Erik Lindahl:
Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold. 1013187 - Szilvia Barsi, Eszter Varga, Daniel Dimitrov, Julio Saez-Rodriguez, László Hunyady, Bence Szalai:
RIDDEN: Data-driven inference of receptor activity from transcriptomic data. 1013188 - Isabella Impalli, Erik Bergland, Chadi M. Saad-Roy, Bryan T. Grenfell, Simon A. Levin, D. G. Joakim Larsson, Ramanan Laxminarayan:
Optimal sampling frequency and site selection for wastewater and environmental surveillance of infectious pathogens: A value of information assessment. 1013190 - Jiaqi Hu, Yixuan Ye, Chi Zhang, Yunfeng Ruan, Pradeep Natarajan, Hongyu Zhao:
Robust pleiotropy-decomposed polygenic scores identify distinct contributions to elevated coronary artery disease polygenic risk. 1013191 - Julia Deichmann, Noam Barda, Michal Canetti, Yovel Peretz, Yael Weiss-Ottolenghi, Yaniv Lustig, Gili Regev-Yochay, Marc Lipsitch:
Predicting antibody kinetics and duration of protection against SARS-CoV-2 following vaccination from sparse serological data. 1013192 - Scott Rich, Taufik A. Valiante, Jérémie Lefebvre:
H- and m-channel overexpression promotes seizure-like events by impairing the ability of inhibitory neurons to process correlated inputs. 1013199 - Gabriella J. Gerlach, Rachel Carrock, Robyn Stix, Elliott J. Stollar, K. Aurelia Ball:
Correction: A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway. 1013201 - Alexander P. Browning, Rebecca M. Crossley, Chiara Villa, Philip K. Maini, Adrianne L. Jenner, Tyler Cassidy, Sara Hamis:
Identifiability of phenotypic adaptation from low-cell-count experiments and a stochastic model. 1013202 - Alexander C. Murph, Graham Casey Gibson, Elizabeth B. Amona, Lauren J. Beesley, Lauren A. Castro, Sara Y. Del Valle, Dave Osthus:
Synthetic method of analogues for emerging infectious disease forecasting. 1013203 - Xixuan Feng, Shuqin Zhang, Limin Li:
OrgaCCC: Orthogonal graph autoencoders for constructing cell-cell communication networks on spatial transcriptomics data. 1013212 - Bart Borghans, Daniel Kortzak, Piersilvio Longo, Bettina Kolen, Jan-Philipp Machtens, Christoph Fahlke:
Allosteric modulation of proton binding confers Cl- activation and glutamate selectivity to vesicular glutamate transporters. 1013214 - Yuxi Long, Bruce Randall Donald:
Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology. 1013216 - Kristen M. Naegle, Jeffrey J. Saucerman, Julie Leonard-Duke, Michael Rariden, Yonathan Tamrat Aberra:
Ten simple rules for effectively assessing lab environments. 1013223 - Yan Miao, Xuan Tang, Chunyu Wang, Zhenyuan Sun, Guohua Wang, Shan Huang:
MVHGCN: Predicting circRNA-disease associations with multi-view heterogeneous graph convolutional neural networks. 1013225 - Christian Leibold, Sebastian Groß:
A mammalian inferior colliculus model for sound source separation using interaural time differences. 1013243
Volume 21, Number 7, 2025
- Kendrick N. Kay, Jacob S. Prince, Thomas Gebhart, Greta Tuckute, Jingyang Zhou, Thomas Naselaris, Heiko H. Schütt:
Disentangling signal and noise in neural responses through generative modeling. 1012092 - Paul Züge, Natalie Schieferstein, Raoul-Martin Memmesheimer:
Cooperative coding of continuous variables in networks with sparsity constraint. 1012156 - Ariel Greiner, José L. Herrera-Diestra, Michael J. Tildesley, Katriona Shea, Matthew J. Ferrari:
Allocating limited surveillance effort for outbreak detection of endemic foot and mouth disease. 1012395 - Jeffrey Keithley, Akash Choudhuri, Bijaya Adhikari, Sriram V. Pemmaraju:
Analyzing greedy vaccine allocation algorithms for metapopulation disease models. 1012539 - Jordan Moutet, Eric Rivals, Fabio Pardi:
Algorithms to reconstruct past indels: The deletion-only parsimony problem. 1012585 - Paul van Lent, Olga Bunkova, Bálint Magyar, Léon Planken, Joep Schmitz, Thomas Abeel:
Jaxkineticmodel: Neural ordinary differential equations inspired parameterization of kinetic models. 1012733 - Alexander Ruys de Perez, Paul E. Anderson, Elena S. Dimitrova, Melissa L. Kemp:
Neural network approaches, including use of topological data analysis, enhance classification of human induced pluripotent stem cell colonies by treatment condition. 1012801 - Catherine House, Ziyi Huang, Kaushik N. Shankar, Sandra J. Young, Meghan E. Roberts, Scott L. Diamond, Maurizio Tomaiuolo, Timothy J. Stalker, Lu Lu, Talid Sinno:
From imaging to computational domains for physics-driven molecular biology simulations: Hindered diffusion in platelet masses. 1012853 - Rachael Aber, Yanming Di, Benjamin D. Dalziel:
Time-series modeling of epidemics in complex populations: Detecting changes in incidence volatility over time. 1012882 - Yann-Stanislas H. M. Barral, Liudmila Polonchuk, Michael Clerx, David J. Gavaghan, Gary R. Mirams, Ken Wang:
Comparison of in silico predictions of action potential duration in response to inhibition of IKr and ICaL with new human ex vivo recordings. 1012913 - Jieyun Bai, Weishan Wang, Xiaoshen Zhang, Hua Lu, Henggui Zhang, Alexander V. Panfilov, Jichao Zhao:
Digital twin for sex-specific identification of class III antiarrhythmic drugs based on in vitro measurements, computer models, and machine learning tools. 1013154 - Mohammad Kayyali, Ana Mincholé, Shuang Qian, Alistair A. Young, Devran Ugurlu, Elliot Fairweather, Steven A. Niederer, John Whitaker, Martin J. Bishop, Pablo Lamata:
Anatomical-electrical coupling of cardiac axes: Definitions and population variability for advancing personalised ECG interpretation. 1013161 - Michaelle E. Dimaggio-Potter, Angelica Velosa, John C. Brent IV, Osmar Del Rio, Eyerusalem F. Abebaw, Fernando Aguilar-Ortega, Dante Rogers, Patrick E. Rothwell, Angeline J. Dukes:
Ten simple rules for thriving in a post-baccalaureate research program. 1013174 - Veronica Martinez Acosta, Carlita Favero, Barbara Lom, Deanne Buffalari, Amy Jo Stavnezer, Leah Chase:
Ten simple rules for faculty members building just and equitable environments in academic science. 1013177 - Isaac W. Vock, Justin W. Mabin, Martin Machyna, Alexandra Zhang, J. Robert Hogg, Matthew D. Simon:
Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite. 1013179 - Nathanael Larigaldie, Tim Yates, Ulrik R. Beierholm:
Perceptual clustering in auditory streaming. 1013189 - Leanna B. Blevins, Amy M. Harrigan, Kevin A. Janes, Jason A. Papin:
Ten simple rules for developing a training program. 1013200 - Probir Kumar Ghosh, Md. Aminul Islam, Md. Ahshanul Haque, Md. Tariqujjaman, Novel Chandra Das, Mohammad Ali, Md. Rasel Uddin, Md. Golam Dostogir Harun:
Identifying predictors and assessing causal effect on hypertension risk among adults using Double Machine Learning models: Insights from Bangladesh Demographic and Health Survey. 1013211 - Josephine Solowiej-Wedderburn, Jennifer T. Pentz, Ludvig Lizana, Bjoern O. Schroeder, Peter A. Lind, Eric Libby:
Competition and cooperation: The plasticity of bacterial interactions across environments. 1013213 - Seth R. Berke, Kanika Kanchan, Mary L. Marazita, Eric Tobin, Ingo Ruczinski:
Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines. 1013215 - Shayna A. Sura, James O. Lloyd-Smith, Peggy Fong:
Herbivore community function shapes resilience and bistability of coral reefs. 1013221 - Tarun Mahajan, Sergei Maslov:
Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome. 1013222 - Thomas Robert Newton, Wilten Nicola:
Comparison of FORCE trained spiking and rate neural networks shows spiking networks learn slowly with noisy, cross-trial firing rates. 1013224 - Albert J. Qü, Lung-Hao Tai, Christopher D. Hall, Emilie M. Tu, Maria K. Eckstein, Karyna Mishchanchuk, Wan Chen Lin, Juliana Chase, Andrew F. Macaskill, Anne G. E. Collins, Samuel J. Gershman, Linda Wilbrecht:
Nucleus accumbens dopamine release reflects Bayesian inference during instrumental learning. 1013226 - Jinsu Kim, Christine Sütterlin, Ming Tan, Germán A. Enciso:
Statistical analysis supports the size control mechanism of Chlamydia development. 1013227 - Shuanglin Jing, Hao Wang:
Infectivity and fatality of influenza in pre- and post-COVID-19 pandemic year. 1013229 - Rui Wang, Tamar Schlick:
How large is the universe of RNA-like motifs? A clustering analysis of RNA graph motifs using topological descriptors. 1013230 - Christo Morison, Dudley Stark, Weini Huang:
Single-cell mutational burden distributions in birth-death processes. 1013241 - Christiaan H. van Dorp, Joshua I. Gray, Daniel H. Paik, Donna L. Farber, Andrew J. Yates:
A variational deep-learning approach to modeling memory T cell dynamics. 1013242 - Christian Brodbeck, Thomas Hannagan, James S. Magnuson:
Recurrent neural networks as neuro-computational models of human speech recognition. 1013244 - Lin Wang, Ting Wang, Xiao-Wei Zhang, Xiao-Fen Lin, Jia Li, Jin-Bao Liao, Rui-Wu Wang:
Evolution of foraging behaviour induces variable complexity-stability relationships in mutualist-exploiter-predator communities. 1013245 - Shingo Gibo, Teiji Kunihiro, Tetsuo Hatsuda, Gen Kurosawa:
Waveform distortion for temperature compensation and synchronization in circadian rhythms: An approach based on the renormalization group method. 1013246 - Aryan Golzaryan, Mohammad Souri, Farshad Moradi Kashkooli, Arman Rahmim, Madjid Soltani:
Multi-scale computational modeling towards efficacy in radiopharmaceutical therapies while minimizing side effects: Modeling of amino acid infusion. 1013247 - Héctor D. García-Verdugo, Cristian Román-Palacios:
LabOps: A flexible self-hosted workflow of open source tools for efficient collaboration within research laboratories. 1013248 - Rose Hartman, Joy Payton, Rose Franzen, Meredith Lee, Elizabeth Drellich, Ali Shokoufandeh, Jeffrey Pennington:
Modular, focused data science education improves biomedical learners' abilities: A study of the Data and Analytics for Research Training (DART) program. 1013249 - Boyu Jiang, Nick Quinn-Bohmann, Christian Diener, Vignesh Bose Nathan, Yu Han-Hallett, Lavanya Reddivari, Sean M. Gibbons, Priyanka Baloni:
Understanding disease-associated metabolic changes in human colonic epithelial cells using the iColonEpithelium metabolic reconstruction. 1013253 - Sarvenaz Sarabipour, Karina Kinghorn, Kaitlyn M. Quigley, Anita Kovacs-Kasa, Brian H. Annex, Victoria L. Bautch, Feilim Mac Gabhann:
Impact of ligand binding on VEGFR1, VEGFR2, and NRP1 localization in human endothelial cells. 1013254 - Aidan Crilly, Alice Malivert, Andreas Christ Sølvsten Jørgensen, Claire E. Heaney, Gema I. Vera Gonzalez, Marcus Ghosh, Manolo Fernandez Perez, Mikael M. Mieskolainen, Mohammed Azzouzi, Zhenzhu Li:
Ten simple rules for navigating AI in science. 1013259 - Sophie Theis, Mario A. Mendieta-Serrano, Bernardo Chapa-y-Lazo, Juliet Chen, Timothy E. Saunders:
CellMet: Extracting 3D shape and topology metrics from confluent cells within tissues. 1013260 - Nobubelo K. Ngandu, Burtram C. Fielding, Peter van Heusden, Kuhle Mcinga, Kriheska Francis, Gordon Harkins:
Population-level toggling of T cell immune escape at human leukocyte antigen anchor residues in SARS-CoV-2 Spike proteins, in an ethnically diverse population region. 1013261 - Cristina S. D. Palma, Daniel J. Haller, Jeffrey J. Tabor, Oleg A. Igoshin:
Changes in Spo0A~P pulsing frequency control biofilm matrix deactivation. 1013263 - Yuhan Li, Nicolò Gozzi, Nicola Perra:
Estimating behavioural relaxation induced by COVID-19 vaccines in the first months of their rollout. 1013266 - Gyeongtae Kim, Pilwon Kim:
Selective inhibition in CA3: A mechanism for stable pattern completion through heterosynaptic plasticity. 1013267 - Junhao Liu, Zeyu Luo, Rui Wang, Xin Li, Yawen Sun, Zongqing Chen, Yu-Juan Zhang:
EUP: Enhanced cross-species prediction of ubiquitination sites via a conditional variational autoencoder network based on ESM2. 1013268 - Jennifer Blanc, Margaret C. Steiner, Lauren E. Blake, Elizabeth Gibbons, Mariadaria K. Ianni-Ravn, Roxroy C. Morgan, Suzanna Parkinson, Christian Porras, Ethan Zhong:
Ten simple rules for success as a trainee-led outreach organization in computational biology education. 1013281 - Kyoko Yoshida, Elsje Pienaar, Shalanda A. Bynum, Naomi C. Chesler, Mitchel J. Colebank, Jessie Heneghan, Nadra Tyus, Jasmine Miller-Kleinhenz, Bruce Y. Lee:
How multi-scale modeling can help examine social determinants of health and resulting disparities. 1013284 - Xiaorui Dong, Du Jiao, Hongzhang Xue, Shiyu Fan, Chaochun Wei:
APAV: An advanced pangenome analysis and visualization toolkit. 1013288 - Robin Vloeberghs, Anne E. Urai, Kobe Desender, Scott W. Linderman:
A Bayesian hierarchical model of trial-to-trial fluctuations in decision criterion. 1013291 - Lars Erik J. Skjegstad, Julius B. Kirkegaard:
Modeling full-scale leaf venation networks. 1013292 - Lan Shui, Anirban Maitra, Ying Yuan, Ken Lau, Harsimran Kaur, Liang Li, Ziyi Li:
PoweREST: Statistical power estimation for spatial transcriptomics experiments to detect differentially expressed genes between two conditions. 1013293 - Quang Dang Nguyen, Sheryl Le Chang, Carl J. E. Suster, Rebecca J. Rockett, Vitali Sintchenko, Tania C. Sorrell, Mikhail Prokopenko:
Multi-scale phylodynamic modelling of rapid punctuated pathogen evolution. 1013295 - Marco Vanoni, Pasquale Palumbo, Federico Papa, Stefano Busti, Laura Gotti, Meike T. Wortel, Bas Teusink, Ivan Orlandi, Alex Pessina, Cristina Airoldi, Luca Brambilla, Marina Vai, Lilia Alberghina:
A modular model integrating metabolism, growth, and cell cycle predicts that fermentation is required to modulate cell size in yeast populations. 1013296 - Hanne Zillmer, Dirk Walther:
Towards a comprehensive view of the pocketome universe - biological implications and algorithmic challenges. 1013298 - Chloe Herman, Evan Bolyen, Anthony Simard, Elizabeth Gehret, J. Gregory Caporaso:
Assessing microbiome engraftment extent following fecal microbiota transplant with q2-fmt. 1013299 - Ruihao Gong, Zijian Feng, Yanyun Zhang:
Using homologous network to identify reassortment risk in H5Nx avian influenza viruses. 1013301 - Yan Yan, Rui Chen, Hakmook Kang, Yuting Tan, Anshul Tiwari, Siyuan Ma, Zhexing Wen, Xue Zhong, Bingshan Li:
Tensor decomposition of multi-dimensional splicing events across multiple tissues to identify splicing-mediated risk genes associated with complex traits. 1013303 - Sofie Verhees, Chandrasekhar Venkataraman, Mariya Ptashnyk:
Mathematical modelling of mechanotransduction via RhoA signalling pathways. 1013305 - Jinming Xiao, Qing Yin, Lei Li, Yao Meng, Xiaobo Liu, Wanrou Hu, Xinyue Huang, Yu Feng, Xiaolong Shan, Weixing Zhao, Peng Wang, Xiaotian Wang, Youyi Li, Huafu Chen, Xujun Duan:
Tracking causal pathways in TMS-evoked brain responses. 1013316 - Pan Li, Sangbo Lee, Kwang-Yeon Choi, Jonathan E. Rubin, Jae Kyoung Kim:
Cardiogenic and chronobiological mechanisms in seizure-induced sinus arrhythmias. 1013318 - Agastya Mondal, Rushil Anirudh, Prashanth Selvaraj:
Multitask deep learning for the emulation and calibration of an agent-based malaria transmission model. 1013330 - Xueqing Peng, Rui Qiao, Peiluan Li, Luonan Chen:
DNFE: Directed network flow entropy for detecting tipping points during biological processes. 1013336 - David J. Degnan, Lisa M. Bramer, Lisa Truong, Robyn L. Tanguay, Sara M. Gosline, Katrina M. Waters:
bmdrc: Python package for quantifying phenotypes from chemical exposures with benchmark dose modeling. 1013337 - Kashif Mahfooz, Mahendra Singh, Robert Renden, John F. Wesseling:
Correction: A Well-Defined Readily Releasable Pool with Fixed Capacity for Storing Vesicles at Calyx of Held. 1013339
Volume 21, Number 8, 2025
- Sakurako Tanida, Kana Fuji, Linjie Lu, Tristan Guyomar, Byung Ho Lee, Alf Honigmann, Anne Grapin-Botton, Daniel Riveline, Tetsuya Hiraiwa, Makiko Nonomura, Masaki Sano:
Predicting organoid morphology through a phase field model: Insights into cell division and lumenal pressure. 1012090 - James G. Lefevre, Brodie A. J. Lawson, Pamela M. Burrage, Diane M. Donovan, Kevin Burrage:
Optimal control of multiple myeloma assuming drug resistance and off-target effects. 1012225 - Yusuke Suita, Hardy Bright, Yuan Pu, Merih Deniz Toruner, Jordan Idehen, Nikos Tapinos, Ritambhara Singh:
Machine learning on multiple epigenetic features reveals H3K27Ac as a driver of gene expression prediction across patients with glioblastoma. 1012272 - Vikas Upadhyay, Mohit Anand, Costas D. Maranas:
novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection. 1012516 - Jo-Yu Liu, James R. H. Cooke, Luc J. P. Selen, W. Pieter Medendorp:
Visuoinertial and visual feedback in online steering control. 1012659 - Farzaneh Darki, James Rankin, Piotr Slowinski:
Tactile stimulations reduce or promote the segregation of auditory streams: psychophysics and modeling. 1012701 - Christine A. Wang, William J. Love, Manuel Jara, Arnoud H. M. van Vliet, Siddhartha Thakur, Cristina Lanzas:
Risk factors for fluoroquinolone- and macrolide-resistance among swine Campylobacter coli using multi-layered chain graphs. 1012797 - Austin Baird, Steven A. White, Erika K. Bisgaard, Rachel K. Wentz, Edward M. Sims, David Hananel:
A model of anaerobic tissue perfusion during trauma - Lactate trajectory curvature can determine recovery. 1012820 - Franco Gino Brunello, Lorenzo Erra, Juan Nicola, Marcelo Adrián Martí:
Integrating AlphaFold2 models and clinical data to improve the assessment of Short Linear Motifs (SLiMs) and their variants' pathogenicity. 1012829 - N. Ezgi Wood, Anil Cengiz, Ming Gao, Alexander V. Ratushny, Ronny Straube:
Mechanistic modeling suggests stroma-targeting antibody-drug conjugates as an alternative to cancer-targeting in cases of heterogeneous target exspression. 1012839 - Dini Wang, Peng Yi, Yiguang Hong, Jie Chen, Gang Yan:
Emergence of cooperation promoted by higher-order strategy updates. 1012891 - Lianxia Li, Unimunkh Uriyanghai, Christine Wai, Hong Yuan, Eric W. Livingston, Edward M. Bahnson, Vinay Sudarsanam, Samuel Haddad, Prabir Roy-Chaudhury, Boyce E. Griffith, Gang Xi:
Temporal evolution of hemodynamics in murine arteriovenous fistula: A micro-CT based CFD study. 1012985 - Yuki Kubota, Taiki Fukiage:
Human-like monocular depth biases in deep neural networks. 1013020 - Isaac J. Stopard, Ellie Sherrard-Smith, Hilary Ranson, Kobié Hyacinthe Toe, Jackie Cook, Joseph Biggs, Ben Lambert, Thomas S. Churcher:
Modelling the effects of adult emergence on the surveillance and age distribution of medically important mosquitoes. 1013035 - Arnab Mutsuddy, Jonah R. Huggins, Aurore K. Amrit, Atalanta Manuela Harley-Gasaway, Cemal Erdem, Evan T. Jones, Olivia G. Laurine, Jon C. Calhoun, Marc R. Birtwistle:
Mechanistic modeling of cell viability assays with in silico lineage tracing. 1013156 - Samuel Torres-Florez, Jorge Luis Flores Anato, Jiahuan Helen He, Vicente Garrido Portilla, Yichen Wu, Mathieu Maheu-Giroux, Etienne Racine, Caroline E. Wagner:
Evaluating COVID-19 vaccination policy in Québec (Canada) using a data-driven dynamic transmission model. 1013207 - R. Tucker Gilman, Cd Durrant, Lucy Malpas, Rebecca N. Lewis:
Does Zipf's law of abbreviation shape birdsong? 1013228 - Anna-Sophie Fiston-Lavier, Emira Cherif, Marie-ka Tilak, Arnaud Soulier, Catherine Breton, Anthony Boureux, Rémy Costa, Xavier Miahle, Clothilde Chenal, Floris Schatt, Camelia Sennaoui, Jean-Christophe Avarre, Anne-Sophie Gosselin-Grenet:
Why and how to set up a Bioinformatics Learning Lab (BILL). 1013236 - Michele Tizzani, Laetitia Gauvin:
Socioeconomic determinants of protective behaviors and contact patterns in the post-COVID-19 pandemic era: A cross-sectional study in Italy. 1013262 - Mikolaj Kocikowski, Marcos Yébenes Mayordomo, Javier Alfaro, Maciej Parys:
Barking up the right tree: Immune checkpoint signatures of human and dog cancers. 1013270 - Matteo Scianna, Riccardo Gallotti, Michele Tizzoni, Oriol Artime, Lucila G. Alvarez Zuzek:
Comparing the effectiveness of ring and block-vaccination strategies on networks. 1013274 - Tracey L. Weissgerber, Natascha Drude, Rima-Maria Rahal, Friederike E. Kohrs:
Ten simple rules for leading a many-author non-empirical paper. 1013283 - Shicong Lei, Yu'an Li, Zheng Ma, Hepeng Zhang, Min Tang:
Identification of the governing equation of stimulus-response data for run-and-tumble dynamics. 1013287 - Jakob C. B. Schwenk, Andrea Alamia:
A hierarchical multiscale model of forward and backward alpha-band traveling waves in the visual system. 1013294 - Gaurav Mendiratta, Kodye Abbott, Yao-Cheng Li, Jingting Yu, Peter Carlip, Melinda Tong, Jianfeng Huang, Maxim N. Shokhirev, Thomas McFall, Geoffrey M. Wahl, Edward C. Stites:
Mathematical modeling suggests 14-3-3 proteins modulate RAF paradoxical activation. 1013297 - Olivia Macmillan-Scott, Mirco Musolesi:
Maynard Smith revisited: A multi-agent reinforcement learning approach to the coevolution of signalling behaviour. 1013302 - Viktoria Zemliak, Gordon Pipa, Pascal Nieters:
Continual familiarity decoding from recurrent connections in spiking networks. 1013304 - Nobuhiko Wagatsuma, Sou Nobukawa, Tomoki Kurikawa:
Excitatory/inhibitory ratio disruption modulates neural synchrony and flow directions in a cortical microcircuit. 1013306 - Friederike E. Kohrs, Natascha Drude, Anita E. Bandrowski, Tracey L. Weissgerber:
Ten simple rules for being a co-author on a many-author non-empirical paper. 1013317 - Matt J. Owen, Gary R. Mirams:
IonBench: A benchmark of optimisation strategies for mathematical models of ion channel currents. 1013319 - Caterina Azzoni, Rene Jüttner, Anje Sporbert, Michael Gotthardt, H. Llewelyn Roderick, Martin Falcke:
Stochastic model of IP3-induced Ca2+ spiking of HEK293 cells. 1013322 - John Kruper, Adam C. Richie-Halford, Joanna Qiao, Asa Gilmore, Kelly Chang, Mareike Grotheer, Ethan Roy, Sendy Caffarra, Teresa Gómez, Sam Chou, Matthew Cieslak, Serge Koudoro, Eleftherios Garyfallidis, Theodore D. Satterthwaite, Jason D. Yeatman, Ariel Rokem:
A software ecosystem for brain tractometry processing, analysis, and insight. 1013323 - Amy Gill, Karina Kinghorn, Victoria L. Bautch, Feilim Mac Gabhann:
Mechanistic computational modeling of sFLT1 secretion dynamics. 1013324 - Robert T. Heussner, Cameron F. Watson, Christopher Z. Eddy, Kunlun Wang, Eric M. Cramer, Allison L. Creason, Gordon B. Mills, Young Hwan Chang:
COEXIST: Coordinated single-cell integration of serial multiplexed tissue images. 1013325 - Tomoko Sakiyama, Akihiro Takahara:
Emergence of a complex network structure on a Spatial Prisoner's Dilemma. 1013329 - Daiki Wakita, Satoshi Yamaji, Daiki Umetsu, Takeshi Kano:
Dual-purpose dynamics emerge from a heterogeneous cell population in Drosophila metamorphosis. 1013331 - Bilal Ahmed, Joshua D. Downer, Brian J. Malone, Joseph G. Makin:
Deep neural networks explain spiking activity in auditory cortex. 1013334 - Yuhang Zhang, Tao Sun, Boyang Zang, Sen Wan:
Decoding decision-making behavior from sparse neural spiking activity. 1013335 - Oswaldo Gressani, Niel Hens:
Nonparametric serial interval estimation with uniform mixtures. 1013338 - Shugang Zhang, Yuntong Li, Wenjian Ma, Qing Cai, Jing Qin, Xiangpeng Bi, Huasen Jiang, Xiaoyu Huang, Zhiqiang Wei:
SuperEdgeGO: Edge-supervised graph representation learning for enhanced protein function prediction. 1013343 - Emily R. Bozich, Xiaolu Guo, Jennifer L. Wilson, Alexander Hoffmann:
A computational workflow for assessing drug effects on temporal signaling dynamics reveals robustness in stimulus-specific NFκB signaling. 1013344 - Weheliye H. Weheliye, Javier Rodriguez, Luigi Feriani, Avelino Javer, Virginie Uhlmann, André E. X. Brown:
A neural network model enables worm tracking in challenging conditions and increases signal-to-noise ratio in phenotypic screens. 1013345 - Xunxun Wang, Ya-Zhou Shi:
3D structure and stability prediction of DNA with multi-way junctions in ionic solutions. 1013346 - Lucas Böttcher, Maria R. D'Orsogna, Tom Chou:
Correction: Aggregating multiple test results to improve medical decision-making. 1013347 - Wenjia Zhou, Junhua Zhang:
Multi-context modeling of driver pathways reveals common and specific mechanisms across 23 cancer types. 1013349 - Bengi Ruken Yavuz, Ugur Sahin, Hyunbum Jang, Ruth Nussinov, Nurcan Tuncbag:
Mutations in tumor signaling, metastases, and synthetic lethality establish distinct patterns. 1013351 - Elliot M. R. Vincent, Edward M. Hill, Stephen Parnell:
Modelling the effectiveness of Integrated Pest Management strategies for the control of Septoria tritici blotch. 1013352 - Eric C. Dykeman:
An empirical model of aminoacylation kinetics for E. coli class I and II aminoacyl tRNA synthetases. 1013353 - Lin Huang, Xiaofei Liu, Fangfang Zhu, Wenwen Min:
Improving cell-type composition inference in spatial transcriptomics with SpaDAMA. 1013354 - Jedrzej Kubica, Sevastianos Korsak, Krzysztof H. Banecki, Dvir Schirman, Anurupa Devi Yadavalli, Ariana Brenner Clerkin, David Kouril, Michal Kadlof, Ben Busby, Dariusz Plewczynski:
The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon. 1013358 - John Robertson, Shorya Consul, Haris Vikalo:
NextVir: Enabling classification of tumor-causing viruses with genomic foundation models. 1013360 - Lauren Stewart, Stephanie Evans, Teresa Brevini, Fotios Sampaziotis, Christopher J. R. Illingworth:
Modelling the potential use of pre-exposure prophylaxis to reduce nosocomial SARS-CoV-2 transmission. 1013361 - Madeline K. Coates, Tudor V. Sava, Sarah M. Tashjian:
Ten simple rules for research with humans. 1013362 - Dimitrios Chalkiadakis, Jaime Sánchez-Claros, Víctor J. López-Madrona, Santiago Canals, Claudio R. Mirasso:
The role of feedforward and feedback inhibition in modulating theta-gamma cross-frequency interactions in neural circuits. 1013363 - Nandan Haloi, Rebecca J. Howard, Erik Lindahl:
Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics. 1013367 - Rongxin Zhang, Wenyong Zhu, Ke Xiao, Jean-Louis Mergny, Xiao Sun:
G4SNVHunter: An R/Bioconductor Package for Evaluating SNV-Induced Disruption of G-Quadruplex Structures Leveraging the G4Hunter Algorithm. 1013368 - Francesca Mastrogiuseppe, Joana Carmona, Christian K. Machens:
Stochastic activity in low-rank recurrent neural networks. 1013371 - Jessica R. Furber, Richard J. Delahay, Ruth Cox, Rosie Woodroffe, Maria O'hagan, Naratip Santitissadeekorn, Stefan Klus, Giovanni Lo Iacono, Mark A. Chambers, David J. B. Lloyd:
Data-driven analysis of fine-scale badger movement in the UK. 1013372 - Thien-Minh Le, Jukka-Pekka Onnela:
Connecting mass-action models and network models for infectious diseases. 1013373 - Jian Peng, Jichuan Quan, Xiaoru Wang:
Integrated pan-cancer analysis of RNA binding protein HuR investigates its biomarker potential in prognosis, immunotherapy, and drug sensitivity. 1013374 - Hui Yuan, Mingzhu Liu, Yushan Qiu, Wai-Ki Ching, Quan Zou:
PLNMFG: Pseudo-label guided non-negative matrix factorization model with graph constraint for single-cell multi-omics data clustering. 1013375 - Margherita Maria Ferrari, Svetlana Poznanovic, Manda Riehl, Jacob Lusk, Stella Hartono, Georgina Gonzalez-Isunza, Frédéric Chedin, Mariel Vázquez, Natasa Jonoska:
The R-loop grammar predicts R-loop formation under different topological constraints. 1013376 - Joanna N. de Klerk, Erin E. Gorsich, John D. Grewar, Benjamin D. Atkins, Warren S. D. Tennant, Karien Labuschagne, Michael J. Tildesley:
Correction: Modelling African horse sickness emergence and transmission in the South African control area using a deterministic metapopulation approach. 1013377 - Michael Weldon, Christian Euler:
Mixotrophy for carbon-conserving waste upcycling. 1013379 - Fenil R. Doshi, Talia Konkle, George A. Alvarez:
A feedforward mechanism for human-like contour integration. 1013391 - Léa Loisel, Vincent Raquin, Maxime Ratinier, Pauline Ezanno, Gaël Beaunée:
Intra-vector infection dynamics challenge how to model the extrinsic incubation period for major arboviruses: dengue, Zika, and chikungunya. 1013393 - Samantha Zink, Songrong Qu, Thomas Holton, Eesha Shankar, Paulina Stanley, David S. Eisenberg, Michael R. Sawaya, Jose A. Rodriguez:
Leveraging structure-informed machine learning for fast steric zipper propensity prediction across whole proteomes. 1013395 - Sunyoung Park, John T. Serences:
Near-random connections support top-down feature-based attentional modulations in early sensory cortex. 1013396 - Farhad Razi, Belén Sancristóbal:
Heterogeneous synaptic homeostasis: A novel mechanism boosting information propagation in the cortex. 1013398 - Bastien Reyné, Tsukushi Kamiya, Ramsès Djidjou-Demasse, Samuel Alizon, Mircea-Traian Sofonea:
Leaky or polarised immunity: Non-Markovian modelling highlights the impact of immune memory assumptions. 1013399 - Mohamed Fawzy, Joseph A. Marsh:
Assessing variant effect predictors and disease mechanisms in intrinsically disordered proteins. 1013400 - Kien Trung Tran, Tran Dang Nguyen, Daniel B. Weissman, Eric Zhewen Li, Sachel Mok, Jennifer L. Small-Saunders, Teun Bousema, Robert J. Zupko, Thu Nguyen-Anh Tran, Maciej F. Boni:
Effects of recombination on multi-drug resistance evolution in Plasmodium falciparum malaria. 1013401 - Amirmahdi Mostofinejad, David A. Romero, Dana Brinson, Thomas K. Waddell, Golnaz Karoubi, Cristina H. Amon:
In silico modeling of directed differentiation of induced pluripotent stem cells to definitive endoderm. 1013407 - Haoran Chen, Yangyuan Zhang, Robert F. Murphy:
CytoSpatio: Learning cell type spatial relationships using multirange, multitype point process models. 1013409 - Moein Khajehnejad, Julian García, Bernd Meyer:
Age polyethism can emerge from social learning: A game-theoretic investigation. 1013415 - Maryam Ghobakhloo, Zahra Ghorbanali, Fatemeh Zare-Mirakabad, Roya Abbaszadeh, Mohammad Taheri-Ledari, Bahman Zeynali:
SimPep and OP-AND: A deep learning framework and curated database for predicting osteogenic peptides. 1013422
Volume 21, Number 9, 2025
- Marina Koutsi, Triantafyllos Stylianopoulos, Fotios Mpekris:
Optimizing therapeutic outcomes with Mechanotherapy and Ultrasound Sonopermeation in solid tumors. 1012676 - Zhaojie Chai, Guansheng Li, Papa Alioune Ndour, Philippe Connes, Pierre A. Buffet, Mélanie Franco, George Em Karniadakis:
In silico biophysics and rheology of blood and red blood cells in Gaucher Disease. 1012705 - Asma Nouira, Chloé-Agathe Azencott:
Sparse multitask group Lasso for genome-wide association studies. 1012734 - Amany Amin, Andrew Philippides, Paul Graham:
Ant visual route navigation: How the fine details of behaviour promote successful route performance and convergence. 1012798 - Franco Pradelli, Giovanni Minervini, Pradeep Venkatesh, Shorya Azad, Hector Gomez, Silvio C. E. Tosatto:
Mathematical modeling and simulation of tumor-induced angiogenesis in retinal hemangioblastoma. 1012799 - Delaney E. Miller, Ashley E. Brown, Nicholas A. Bianco, Rucha Bhise, Scott L. Delp, Steven H. Collins:
How peak knee loads are affected by changing the mass of lower-limb body segments during walking. 1012833 - Israël Tankam-Chedjou, Ruairi Donnelly, Christopher A. Gilligan:
Optimizing crop varietal mixtures for viral disease management: A case study on cassava virus epidemics. 1012842 - Jennifer D. Senta, Sonia J. Bishop, Anne G. E. Collins:
Dual process impairments in reinforcement learning and working memory systems underlie learning deficits in physiological anxiety. 1012872 - Hunter L. Colegrove, Raymond J. Monnat Jr., Alison F. Feder:
Epithelial competition determines gene therapy potential to suppress Fanconi Anemia oral cancer risk. 1012915 - Kamil Ksiazek, Wilhelm Masarczyk, Przemyslaw Glomb, Michal Romaszewski, Krisztián Búza, Przemyslaw Sekula, Michal Cholewa, Katarzyna Kolodziej, Piotr Gorczyca, Magdalena Piegza:
Deep learning approach for automatic assessment of schizophrenia and bipolar disorder in patients using R-R intervals. 1012983 - Jordy Peeters, Dimitri De Bundel, Kenno Vanommeslaeghe:
Molecular dynamics study of differential effects of serotonin-2A-receptor (5-HT2AR) modulators. 1013000 - Yen-Ju Chen, Zitang Sun, Shin'ya Nishida:
Human visual grouping based on within- and cross-area temporal correlations. 1013001 - Long Xu, Qiang Yang, Weihe Dong, Xiaokun Li, Kuanquan Wang, Suyu Dong, Gongning Luo, Xianyu Zhang, Tiansong Yang, Xin Gao, Guohua Wang:
THLANet: A deep learning framework for predicting TCR-pHLA binding in immunotherapy applications. 1013050 - Andrew Patton, Jörn Davidsen:
Changing cognitive chimera states in human brain networks with age: Variations in cognitive integration and segregation. 1013093 - Adel Heydarabadipour, Lucian P. Smith, Joseph L. Hellerstein, Herbert M. Sauro:
SBMLNetwork: A framework for standards-based visualization of biochemical models. 1013128 - Jinrui Ma, Xingyu Liu, Zengwen He, Haohao Zhang, Yonghui Ma, Ziqiu Fan, Xuehui Zhao, Ji Zhi, Qing Cao, Huiwen Xue, Huitian Gou:
Optimization of echinococcosis control measures based on system dynamics. 1013186 - Ricardo Roopnarinesingh, Neel D. Jani, Michelle Leppert, Debanjan Mukherjee:
Understanding thromboembolus transport patterns in the brain for stroke in the presence of carotid artery stenosis. 1013269 - Pierre Orhan, Yves Boubenec, Jean-Rémi King:
The detection of algebraic auditory structures emerges with self-supervised learning. 1013271 - Marco Saltini, Eva E. Deinum:
Microtubule-based nucleation results in a large sensitivity to cell geometry of the plant cortical array. 1013282 - Marco Ruscone, Eirini Tsirvouli, Andrea Checcoli, Dénes Türei, Emmanuel Barillot, Julio Saez-Rodriguez, Loredana Martignetti, Åsmund Flobak, Laurence Calzone:
NeKo: A tool for automatic network construction from prior knowledge. 1013300 - Zhiqiang Ma, Ran Chen, Zibo Feng:
Exploration of potential novel drug targets for rheumatoid arthritis by plasma proteome screening. 1013333 - Matthias Bruhns, Jan T. Schleicher, Maximilian Wirth, Marcello Zago, Sepideh Babaei, Manfred Claassen:
Effects of segmentation errors on downstream-analysis in highly-multiplexed tissue imaging. 1013350 - Ben Kawam, Julia Ostner, Richard McElreath, Oliver Schülke, Daniel Redhead:
A causal framework for the drivers of animal social network structure. 1013370 - Maxime Calka, Pierre Badin, Mohammad Ali Nazari, Michel Rochette, Pascal Perrier, Yohan Payan:
The G-OBIM tongue model: An accurate open-source biomechanical model of a male human tongue. 1013378 - Giuseppe Agapito, Mario Cannataro, Pietro Cinaglia, Marianna Milano:
Ten practical tips and tricks to improve the effectiveness of biological network alignment. 1013386 - Matthew Aguirre, Jeffrey P. Spence, Guy Sella, Jonathan K. Pritchard:
Gene regulatory network structure informs the distribution of perturbation effects. 1013387 - Jianing Yang, Gregory R. Grant, Thomas G. Brooks:
Generating correlated data for omics simulation. 1013392 - Gui Araujo, Miguel Lurgi:
Mutualism provides a basis for biodiversity in eco-evolutionary community assembly. 1013402 - Tristan M. Stöber, Andrew B. Lehr, Arash Nikzad, Mohammad Ganjtabesh, Marianne Fyhn, Arvind Kumar:
Competition and cooperation of assembly sequences in recurrent neural networks. 1013403 - Meirian Lovelace-Tozer, John Brown, Robert S. Clemens, Kathryn Greenhill, Fathima Haseen, Danny Kingsley, Ellen A. Lyrtzis, Katherine Mills, Giorgia Mori, Kathryn M. Steel, Liz Stokes, Kathryn Unsworth, Adeline L. H. Wong, Amany Gouda-Vossos:
Ten simple rules for training by researchers for researchers in a rapidly evolving workforce. 1013408 - Rui Yin, Alba Gutiérrez-Sacristán, Shilpa Nadimpalli Kobren, Paul Avillach:
VarPPUD: Pinpointing diagnostic variants from sets of prioritized, strong candidate variants. 1013414 - Ghislain St-Yves, Kendrick N. Kay, Thomas Naselaris:
Variation in the geometry of concept manifolds across human visual cortex. 1013416 - Kristi Lin-Rahardja, Jessica Scarborough, Jacob G. Scott:
Personalizing chemotherapy drug selection using a novel transcriptomic chemogram. 1013417 - Lucy Goodfellow, Carl A. B. Pearson, Simon R. Procter:
paramix: An R package for parameter discretisation in compartmental models, with application to calculating years of life lost. 1013420 - Nicola F. Müller, Remco R. Bouckaert, Chieh-Hsi Wu, Trevor Bedford:
MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions. 1013421 - Tong Xiao, Ying Liu, Kaimiao Hu, Kaimin Guo, Mengying Zhang, Tingting Wang, Weihua Lei, Wenjia Wang, Shuiping Zhou, Yunhui Hu, Ran Su:
Drug-induced liver injury prediction based on graph convolutional networks and toxicogenomics. 1013423 - Gowri Nayar, Alp Tartici, Russ B. Altman:
Paying attention to attention: High attention sites as indicators of protein family and function in language models. 1013424 - Madison Shoraka, Herby Jean-Baptiste, Bettina Buttaro, Gillian Queisser:
Using stochastic cellular automata to model and define sufficient conditions for the survival of Enterococcus faecalis biofilms with the pCF10 plasmid under erythromycin treatment. 1013425 - Sandor Beregi, Kris V. Parag:
Optimal algorithms for controlling infectious diseases in real time using noisy infection data. 1013426 - Daniel R. Bergman, Trachette Jackson, Harsh Vardhan Jain, Kerri-Ann Norton:
An efficient and flexible framework for inferring global sensitivity of agent-based model parameters. 1013427 - E. Yagmur Erten, Marc Tollis, Hanna Kokko:
Shrinking to bird size with dinosaur-level cancer defences: Evolution of cancer suppression over macroevolutionary time. 1013432 - Marco Garcia Noceda, Gargi Kher, Shikhar Uttam, John P. Barton:
Clonal heterogeneity and antigenic stimulation shape persistence of the latent reservoir of HIV. 1013433 - Mintu Nandi, Shashank Shekhar, Sandeep Choubey:
A generalized theoretical framework to investigate multicomponent actin dynamics. 1013434 - Kristopher Nolte, Jan Baumbach, Christian Lins, Jens Johann Georg Lohmann, Philip Kollmannsberger, Felix Gregor Sauer, Renke Lühken:
Potentials and limitations in the application of Convolutional Neural Networks for mosquito species identification using wing images. 1013435 - Narmada Sambaturu, Zena Lapp, Fernando D. K. Tria, Ethan O. Romero-Severson, Carmen Molina-París, Thomas Leitner:
wavess: An R package for simulation of adaptive within-host virus sequence evolution. 1013437 - Dongju Lim, Kyeong Tae Ko, Hyukpyo Hong, Hyojung Lee, Boseung Choi, Won Chang, Sunhwa Choi, Jae Kyoung Kim:
A history-dependent approach for accurate initial condition estimation in epidemic models. 1013438 - Bevelynn Whaler, Grant Lythe, Joseph Gillard, Thomas R. Laws, Jonathan Carruthers, Thomas Finnie, Carmen Molina-París, Martín López-García:
Mechanistic within-host mathematical model of inhalational anthrax. 1013439 - Xuwen Wang, Yanfang Guan, Wei Gao, Xin Lai, Wuqiang Cao, Xiaoyan Zhu, Xiaoling Zeng, Yuqian Liu, Shenjie Wang, Ruoyu Liu, Xin Yi, Shuanying Yang, Jiayin Wang:
MRDtarget: A heuristic Gaussian approach for optimizing targeted capture regions to enhance Minimal Residual Disease detection. 1013443 - Shuze Liu, Samuel Joseph Gershman:
Action subsampling supports policy compression in large action spaces. 1013444 - Boluwatife Ikwunne, Jolie Parham, Erdem Pulcu:
A nonlinear relationship between prediction errors and learning rates in human reinforcement-learning. 1013445 - Anton Iyer, Adrian Alva, Adrián E. Granada, Shaon Chakrabarti:
Inheritable cell-states shape drug-persister correlations and population dynamics in cancer cells. 1013446 - Joseph James Tharayil, Ciro Zinno, Filippo Agnesi, Bryn A. Lloyd, Silvia Farcito, Antonino Cassara, Niels Kuster, Michael Reimann, Silvestro Micera, Esra Neufeld:
Simulation insights on the compound action potential in multifascicular nerves. 1013452 - Jaroslav Zak, Ian Newman, Daniel J. Montiel Garcia, Daniele Parisi, Janet Joy, Steven R. Head, Jean-Christophe Ducom, Padmaja Natarajan, Haissi Cui, Sabah Ul-Hasan:
Catalyzing computational biology research at an academic institute through an interest network. 1013453 - William L. Tong, Venkatesh N. Murthy, Gautam Reddy:
Adaptive algorithms for shaping behavior. 1013454 - Eduardo G. Zilves, Lucas O. Müller, Gonzalo D. Maso Talou, Vladimir Hachinski, John David Spence, Pablo J. Blanco:
Blood flow in the human cerebral cortex: Large-scale pial vascularization and 1D simulation. 1013459 - Eric V. Strobl, Eric R. Gamazon:
Transcriptome-wide root causal inference. 1013461 - Jiancheng Zhang, Xiangting Li, Xiaolu Guo, Zhaoyi You, Lucas Böttcher, Alex Mogilner, Alexander Hoffmann, Tom Chou, Mingtao Xia:
Reconstructing noisy gene regulation dynamics using extrinsic-noise-driven neural stochastic differential equations. 1013462 - David Hodgson, James Hay, Sheikh Jarju, Dawda Jobe, Rhys Wenlock, Thushan I. de Silva, Adam J. Kucharski:
serojump: A Bayesian tool for inferring infection timing and antibody kinetics from longitudinal serological data. 1013467 - Giulia Mazzi, Ambra Ferrari, Maria Laura Mencaroni, Chiara Valzolgher, Mirko Tommasini, Francesco Pavani, Stefania Benetti:
Prior expectations guide multisensory integration during face-to-face communication. 1013468 - Kwangjun Lee, Cyriel M. A. Pennartz, Jorge F. Mejías:
Cortical networks with multiple interneuron types generate oscillatory patterns during predictive coding. 1013469 - Anastasia Lucas, Daniel E. Schäffer, Jayamanna Wickramasinghe, Noam Auslander:
kMermaid: Ultrafast metagenomic read assignment to protein clusters by hashing of amino acid k-mer frequencies. 1013470 - Ruben Sanchez-Romero, Sibel Akyuz, Bart Krekelberg:
EFMouse: A toolbox to model stimulation-induced electric fields in the mouse brain. 1013471 - Peng Tao, Yunda Si, Jie Xia, Yi Xiao:
Transcription reshapes RNA hairpin folding pathways revealed by all-atom molecular dynamics simulations. 1013472 - Sarah M. Burbach, Bryan Briney:
A curriculum learning approach to training antibody language models. 1013473 - Azka Javaid, H. Robert Frost:
Mouse-Specific Single cell cytokine activity prediction and Estimation (MouSSE). 1013475 - Rebekka Heinen, Elias M. B. Rau, Nora A. Herweg, Nikolai Axmacher:
Task-relevant representational spaces in human memory traces. 1013476 - Yam Fung Hilaire Cheung, Chukiat Tantiwong, Dipali Kale, Jonathan M. Gibbins, Steve P. Watson, Johan W. M. Heemskerk, Albert Sickmann, Robert Ahrends, Joanne L. Dunster:
A computational framework for the investigation of phosphoinositide regulation. 1013477 - Linh Truong, Thao Truong, Huy Nguyen:
OmnibusX: A unified platform for accessible multi-omics analysis. 1013480 - Ronald Galiwango, Christopher J. Whalen, Grace Kebirungi, Mugume T. Atwine, Rodgers Kimera, Alfred Ssekagiri, Timothy W. Kimbowa, Edward Lukyamuzi, Mike Nsubuga, Lloyd Ssentongo, Henry Mutegeki, John M. Fonner, Frank Wuerthwein, Ari Berman, Laura B. Okalebo, Meghan Coakley McCarthy, Victor S. Kramer, Mariam Quiñones, Phillip Cruz, Darrell E. Hurt, Maria Y. Giovanni, Nicola J. Mulder, Michael Tartakovsky, Jonathan K. Kayondo, Daudi Jjingo:
Ten simple rules for building and maintaining sustainable high-performance computing infrastructure for research in resource-limited settings. 1013481 - Théotime Grohens, Sam Meyer, Guillaume Beslon:
Emergence of supercoiling-mediated regulatory networks through the evolution of bacterial chromosome organization. 1013482 - Futa Tomita, Jun-nosuke Teramae:
Dynamical mean-field theory for a highly heterogeneous neural population with graded persistent activity of the entorhinal cortex. 1013484 - Yinan Xu, Chantel S. Prat, Florian Sense, Hedderik van Rijn, Andrea Stocco:
Default mode network connectivity predicts individual differences in long-term forgetting: Evidence for storage degradation, not retrieval failure. 1013485 - Yanqing Dong, Jing Wei, Songjun Peng, Xinran Wu, Yaru Xu, Jianfeng Feng, Jie Zhang, Viktor K. Jirsa, Jie Xiang:
Effects of tDCS of the DLPFC on brain networks: A hybrid brain modeling study. 1013486 - Bangyi Zhang, Yun Zuo, Jun Wan, Jiayue Liu, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng:
HyperACP: A cutting-edge hybrid framework for anticancer peptide classification via scalable feature extraction and adaptive neighbor-based synthesis. 1013489 - Samuel Cure, Florian G. Pflug, Simone Pigolotti:
Fast and exact stochastic simulations of epidemics on static and temporal networks. 1013490 - Dennis N. Makau, Jonathan Arzt, Kimberly Vanderwaal:
Opportunities for machine learning to predict cross-neutralization in FMDV serotype O. 1013491 - Giacomo Severini, David Muñoz:
A physiologically inspired hybrid CPG/Reflex controller for cycling simulations that generalizes to walking. 1013494 - William Jeffries, Bryan M. Delfing, Xavier E. Laracuente, Xingyu Luo, Audrey Olson, Kenneth W. Foreman, Kyung Hyeon Lee, Greg Petruncio, Vito De Benedictis, Mikell Paige, Kylene Kehn-Hall, Christopher Lockhart, Dmitri K. Klimov:
Ligands binding diffusively to protein target act as inhibitors of protein-protein interactions. 1013495 - Veronica Pisu, Erich W. Graf, Wendy J. Adams:
The size-weight illusion and beyond: A new model of perceived weight. 1013496 - Leandro P. L. Jacob, Sydney M. Bailes, Stephanie D. Williams, Carsen Stringer, Laura D. Lewis:
Brainwide hemodynamics predict EEG neural rhythms across sleep and wakefulness in humans. 1013497 - Kamil Wolos, Leszek Pstras, Urszula Bialonczyk, Malgorzata Debowska, Wojciech Dabrowski, Dorota Siwicka-Gieroba, Jan Poleszczuk:
Personalized pulse wave propagation modeling to improve vasopressor dosing management in patients with severe traumatic brain injury. 1013501 - Jantien A. Backer, Don Klinkenberg, Fuminari Miura, Jacco Wallinga:
Estimating the effectiveness of non-pharmaceutical interventions against COVID-19 transmission in the Netherlands. 1013502 - Han-Jia Jiang, Jugoslava Acimovic, Tiina Manninen, Iiro Ahokainen, Jonas Stapmanns, Mikko Lehtimäki, Markus Diesmann, Sacha J. van Albada, Hans Ekkehard Plesser, Marja-Leena Linne:
Modeling neuron-astrocyte interactions in neural networks using distributed simulation. 1013503 - Dimitrios G. Patsatzis, Efstathios-Al. Tingas, S. Mani Sarathy, Dimitris A. Goussis, Renaud B. Jolivet:
Elucidating reaction dynamics in a model of human brain energy metabolism. 1013504 - John M. Drake, Barbara A. Han:
How to write a scientific paper in fifteen steps. 1013505 - Tshikala Eddie Lulamba, Themba Mutemaringa, Nicki Tiffin:
Ten quick tips for protecting health data using de-identification and perturbation of structured datasets. 1013507 - Tianyong Yao, Ruby Kim:
Mathematical modeling of dopamine rhythms and timing of dopamine reuptake inhibitors. 1013508 - Priyata Kalra, Bastian Kister, Rebekka Fendt, Mario Köster, Julia Pulverer, Sven Sahle, Lars Kuepfer, Ursula Kummer:
A comparative computational analysis of IFN-alpha pharmacokinetics and its induced cellular response in mice and humans. 1013509 - Biplab Maity, Swarnendu Banerjee, Abhishek Senapati, Jon Pitchford, Joydev Chattopadhyay:
Coupling plankton and cholera dynamics: Insights into outbreak prediction and practical disease management. 1013523 - Joshua Looker, Kat S. Rock, Louise Dyson:
Identifying COVID-19 peaks using early warning signals. 1013524 - Ruizhi Yuan, Ziqi Rong, Haoran Hu, Tianhao Liu, Shiyue Tao, Wei Chen, Lu Tang:
Harmony-based data integration for distributed single-cell multi-omics data. 1013526 - Yun Lin, James A. Hay, Yu Meng, Benjamin J. Cowling, Bingyi Yang:
Generalizing population RT-qPCR cycle threshold values-informed estimation of epidemiological dynamics: Impact of surveillance practices and pathogen variability. 1013527 - Hojin Jang, Frank Tong:
Category-specific perceptual learning of robust object recognition modelled using deep neural networks. 1013529 - Correction: Design of field trials for the evaluation of transmissible vaccines in animal populations. 1013530
- Caroline Mburu, John Ojal, Rose Selim, Rose Ombati, Donald Akech, Boniface Karia, James Tuju, Antipa Sigilai, Gaby Smits, Pieter van Gageldonk, Fiona van der Klis, Eunice Kagucia, Anthony Scott, Ifedayo M. O. Adetifa, Stefan Flasche:
Modelling the relative contribution of infection, routine vaccination and supplementary immunisation activities to measles seroconversion in Kenyan Children. 1013531 - Paolo Pigini, Federico Manuel Giorgi, Keng Boon Wee:
Utargetome: A targetome prediction tool for modified U1-snRNAs to identify distal-target positions with improved selectivity. 1013534 - Correction: Success-efficient/failure-safe strategy for hierarchical reinforcement motor learning. 1013537
- Yichao Liu, Peter Fransson, Julian Heidecke, Prasad Liyanage, Jonas Wallin, Joacim Röcklov:
An explainable covariate compartmental model for predicting the spatio-temporal patterns of dengue in Sri Lanka. 1013540 - Richard Schweitzer, Thomas Seel, Jörg Raisch, Martin Rolfs:
Early visual signatures and benefits of intra-saccadic motion streaks. 1013544 - Congqiang Gao, Chenghui Yang, Lihua Zhang:
A graph neural network-based spatial multi-omics data integration method for deciphering spatial domains. 1013546