Plos Computational Biology

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  Publication Venue For

  • Generative models of birdsong learning link circadian fluctuations in song variability to changes in performance..  19:e1011051. 2023
  • Multi-view clustering by CPS-merge analysis with application to multimodal single-cell data..  19:e1011044. 2023
  • Bayesian reconstruction of memories stored in neural networks from their connectivity..  19:e1010813. 2023
  • Omitting age-dependent mosquito mortality in malaria models underestimates the effectiveness of insecticide-treated nets..  18:e1009540. 2022
  • Optimal anti-amyloid-beta therapy for Alzheimer's disease via a personalized mathematical model..  18:e1010481. 2022
  • TAMC: A deep-learning approach to predict motif-centric transcriptional factor binding activity based on ATAC-seq profile..  18:e1009921. 2022
  • Non-monotonic effects of GABAergic synaptic inputs on neuronal firing..  18:e1010226. 2022
  • Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus..  18:e1009855. 2022
  • Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts..  18:e1009811. 2022
  • Measuring and mitigating PCR bias in microbiota datasets..  17:e1009113. 2021
  • Can subjective pain be inferred from objective physiological data? Evidence from patients with sickle cell disease..  17:e1008542. 2021
  • Causal network inference from gene transcriptional time-series response to glucocorticoids..  17:e1008223. 2021
  • Response nonlinearities in networks of spiking neurons..  16:e1008165. 2020
  • Identifying determinants of persistent MRSA bacteremia using mathematical modeling..  15:e1007087. 2019
  • Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features..  15:e1006952. 2019
  • A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations..  15:e1006564. 2019
  • meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays..  14:e1006506. 2018
  • Principles that govern competition or co-existence in Rho-GTPase driven polarization..  14:e1006095. 2018
  • Clustering gene expression time series data using an infinite Gaussian process mixture model..  14:e1005896. 2018
  • Neuron's eye view: Inferring features of complex stimuli from neural responses..  13:e1005645. 2017
  • Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective..  13:e1005352. 2017
  • Ten Simple Rules for Effective Statistical Practice..  12:e1004961. 2016
  • Beyond the E-Value: Stratified Statistics for Protein Domain Prediction..  11:e1004509. 2015
  • Random Wiring, Ganglion Cell Mosaics, and the Functional Architecture of the Visual Cortex..  11:e1004602. 2015
  • A Three-Threshold Learning Rule Approaches the Maximal Capacity of Recurrent Neural Networks..  11:e1004439. 2015
  • Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes..  11:e1004429. 2015
  • Evaluating Spatial Interaction Models for Regional Mobility in Sub-Saharan Africa..  11:e1004267. 2015
  • Bacterial temporal dynamics enable optimal design of antibiotic treatment..  11:e1004201. 2015
  • HPV clearance and the neglected role of stochasticity..  11:e1004113. 2015
  • Modulation of network excitability by persistent activity: how working memory affects the response to incoming stimuli..  11:e1004059. 2015
  • Estimating relative changes of metabolic fluxes..  10:e1003958. 2014
  • Memory maintenance in synapses with calcium-based plasticity in the presence of background activity..  10:e1003834. 2014
  • Memory capacity of networks with stochastic binary synapses..  10:e1003727. 2014
  • Mathematical modeling of the Phoenix Rising pathway..  10:e1003461. 2014
  • Estimating the probability of polyreactive antibodies 4E10 and 2F5 disabling a gp41 trimer after T cell-HIV adhesion..  10:e1003431. 2014
  • Angiogenesis: an adaptive dynamic biological patterning problem..  9:e1002983. 2013
  • Hierarchical modeling for rare event detection and cell subset alignment across flow cytometry samples..  9:e1003130. 2013
  • Leveraging prior information to detect causal variants via multi-variant regression..  9:e1003093. 2013
  • Optimal properties of analog perceptrons with excitatory weights..  9:e1002919. 2013
  • Osteoprotegerin in bone metastases: mathematical solution to the puzzle..  8:e1002703. 2012
  • Storage of correlated patterns in standard and bistable Purkinje cell models..  8:e1002448. 2012
  • The role of local backrub motions in evolved and designed mutations..  8:e1002629. 2012
  • The statistics of bulk segregant analysis using next generation sequencing..  7:e1002255. 2011
  • Automatic annotation of spatial expression patterns via sparse Bayesian factor models..  7:e1002098. 2011
  • Digital atlasing and standardization in the mouse brain..  7:e1001065. 2011
  • From spiking neuron models to linear-nonlinear models..  7:e1001056. 2011
  • Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs..  6:e1001037. 2010
  • Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies..  6:e1000955. 2010
  • Latent factor analysis to discover pathway-associated putative segmental aneuploidies in human cancers..  6:e1000920. 2010
  • Enhancement of transport selectivity through nano-channels by non-specific competition..  6:e1000804. 2010
  • Maturation of GABAergic inhibition promotes strengthening of temporally coherent inputs among convergent pathways..  6:e1000797. 2010
  • Enhancement of transport selectivity through nano-channels by non-specific competition..  6:e1000804. 2010
  • The dynamics of T-cell receptor repertoire diversity following thymus transplantation for DiGeorge anomaly..  5:e1000396. 2009
  • Structural adaptation and heterogeneity of normal and tumor microvascular networks..  5:e1000394. 2009
  • A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale..  5:e1000334. 2009
  • Encoding of naturalistic stimuli by local field potential spectra in networks of excitatory and inhibitory neurons..  4:e1000239. 2008
  • Noise reduction by diffusional dissipation in a minimal quorum sensing motif..  4:e1000167. 2008
  • Regulation of signal duration and the statistical dynamics of kinase activation by scaffold proteins..  4:e1000099. 2008
  • Modeling cancer progression via pathway dependencies..  4:e28. 2008
  • Coping with viral diversity in HIV vaccine design: a response to Nickle et al..  4:e15. 2008
  • Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events..  4:e21. 2008
  • Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events..  4:e21. 2008
  • Comparative genomics search for losses of long-established genes on the human lineage..  3:e247. 2007
  • A nucleosome-guided map of transcription factor binding sites in yeast..  3:e215. 2007
  • STDP in a bistable synapse model based on CaMKII and associated signaling pathways..  3:e221. 2007
  • Efficiency, selectivity, and robustness of nucleocytoplasmic transport..  3:e125. 2007
  • Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites..  3:e90. 2007
  • Efficiency, selectivity, and robustness of nucleocytoplasmic transport..  3:e125. 2007
  • Computational inference of neural information flow networks..  2:e161. 2006