A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System by Liu, Bing, Zhang, Jing, Tan, Pei Yi, Hsu, David, Blom, Anna M., Leong, Benjamin, Sethi, Sunil, Ho, Bow, Ding, Jeak Ling, Thiagarajan, P. S.

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A Granger Causality Measure for Point Process Models of Ensemble Neural Spiking Activity by Kim, Sanggyun, Putrino, David, Ghosh, Soumya, Brown, Emery N.

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How Haptic Size Sensations Improve Distance Perception by Battaglia, Peter W., Kersten, Daniel, Schrater, Paul R.

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Inferring Correlation Networks from Genomic Survey Data by Friedman, Jonathan, Alm, Eric J.

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Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology by Toni, Tina, Tidor, Bruce

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Shape Similarity, Better than Semantic Membership, Accounts for the Structure of Visual Object Representations in a Population of Monkey Inferotemporal Neurons by Baldassi, Carlo, Alemi-Neissi, Alireza, Pagan, Marino, Zecchina, Riccardo, Zoccolan, Davide, DiCarlo, James

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An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding by Mahony, Shaun, Edwards, Matthew D, Mazzoni, Esteban O, Sherwood, Richard I, Kakumanu, Akshay, Morrison, Carolyn A, Wichterle, Hynek, Gifford, David K

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Patient contrastive learning: A performant, expressive, and practical approach to electrocardiogram modeling by Diamant, Nathaniel, Reinertsen, Erik, Song, Steven, Aguirre, Aaron D, Stultz, Collin M, Batra, Puneet

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Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli by Morris, Melody Kay, Saez-Rodriguez, Julio, Clarke, David C., Sorger, Peter K., Lauffenburger, Douglas A.

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Minimal Size of Cell Assemblies Coordinated by Gamma Oscillations by Borgers, Christoph, LeBeau, Fiona E. N., Boyden, Edward Stuart, Kopell, Nancy J., Franzesi, Giovanni Talei

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State-Space Analysis of Time-Varying Higher-Order Spike Correlation for Multiple Neural Spike Train Data by Shimazaki, Hideaki, Amari, Shun-ichi, Brown, Emery N., Grun, Sonja

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Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome by Abubucker, Sahar, Segata, Nicola, Goll, Johannes, Schubert, Alyxandria M., Izard, Jacques, Cantarel, Brandi L., Rodriguez-Mueller, Beltran, Zucker, Jeremy, Thiagarajan, Mathangi, Henrissat, Bernard, White, Owen, Kelley, Scott T., Methe, Barbara, Schloss, Patrick D., Gevers, Dirk, Mitreva, Makedonka, Huttenhower, Curtis

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High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints by Guo, Yuchun, Mahony, Shaun

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Dynamic Modeling of Cell Migration and Spreading Behaviors on Fibronectin Coated Planar Substrates and Micropatterned Geometries by Kim, Min-Cheol, Kamm, Roger Dale, Neal, Devin M, Asada, Haruhiko

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Fine-scale estimation of effective reproduction numbers for dengue surveillance by Ong, Janet, Soh, Stacy, Ho, Soon Hoe, Seah, Annabel, Dickens, Borame Sue, Tan, Ken Wei, Koo, Joel Ruihan, Cook, Alex R., Richards, Daniel R., Gaw, Leon Yan-Feng, Ng, Lee Ching, Lim, Jue Tao

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Teasing apart translational and transcriptional components of stochastic variations in eukaryotic gene expression by Przytycka, Teresa M., Salari, Raheleh, Wojtowicz, Damian, Zheng, Jie, Levens, David, Pilpel, Yitzhak

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Interplay between topology and dynamics in excitation patterns on hierarchical graphs by Marc Hütt, Annick Lesne

“…In a recent publication [Müller-Linow et al. (2008) PLoS Computational Biology 4, 1000190] two types of correlations between network topology and dynamics have been observed: waves propagating from central nodes and module-based synchronization. …”
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Female Dynamics in Authorship of Scientific Publications in the Public Library of Science: A 10-year Bibliometric Analysis of Biomedical Research by Panagiotis Giannos, Konstantinos Katsikas Triantafyllidis, Maria Paraskevaidi, Maria Kyrgiou, Konstantinos S. Kechagias

“…Publications from seven exemplar cross-specialty journals of the Public Library of Science (<i>PLoS Medicine, PLoS Biology, PLoS One, PLoS Computational Biology, PLoS Genetics, PLoS Pathogens, and PLoS Neglected Tropical Diseases</i>) between January 2010 and December 2020 were extracted from Web of Science. …”
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Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data by Mitsos, Alexander, Melas, Ioannis N., Siminelakis, Paraskeuas, Chairakaki, Aikaterini D., Saez-Rodriguez, Julio, Alexopoulos, Leonidas G.

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MCAM: Multiple Clustering Analysis Methodology for Deriving Hypotheses and Insights from High-Throughput Proteomic Datasets by Naegle, Kristen Marie, White, Forest M., Welsch, Roy E, Yaffe, Michael B, Lauffenburger, Douglas A

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