All Stories

  1. Protein Language Models Capture Structural and Functional Epistasis in a Zero-Shot Setting
  2. Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome
  3. Evolutionary chemical learning in dimerization networks
  4. Predicting metabolite response to dietary intervention using deep learning
  5. noSpliceVelo infers gene expression dynamics without separating unspliced and spliced transcripts
  6. noSpliceVelo infers gene expression dynamics without separating unspliced and spliced transcripts
  7. DR-BERT: A protein language model to annotate disordered regions
  8. Fitness advantage of sequential metabolic strategies emerges from community interactions in strongly fluctuating environments
  9. Higher-Order Interactions in Auxotroph Communities Enhance Their Resilience to Resource Fluctuations
  10. Semi-quantitative group testing for efficient and accurate qPCR screening of pathogens with a wide range of loads
  11. Emergence of catalytic function in prebiotic information-coding polymers
  12. Emergence of catalytic function in prebiotic information-coding polymers
  13. Coarse-Grained Model of Serial Dilution Dynamics in Synthetic Human Gut Microbiome
  14. A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains
  15. Emergence of catalytic function in prebiotic information-coding polymers
  16. FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi
  17. The ecological consequences of microbial metabolic strategies in fluctuating environments
  18. Functional convergence in slow-growing microbial communities arises from thermodynamic constraints
  19. Emergence of catalytic function in prebiotic information-coding polymers
  20. Predicting metabolite response to dietary intervention using deep learning
  21. Predicting metabolomic profiles from microbial composition through neural ordinary differential equations
  22. DR-BERT: A Protein Language Model to Annotate Disordered Regions
  23. Fine-scale diversity of microbial communities due to satellite niches in boom and bust environments
  24. Predicting metabolomic profiles from microbial composition through neural ordinary differential equations
  25. FUN-PROSE: A Deep Learning Approach to Predict Condition-Specific Gene Expression in Fungi
  26. Mitigation of SARS-CoV-2 transmission at a large public university
  27. Fine-scale diversity of microbial communities due to satellite niches in boom-and-bust environments
  28. Functional convergence in slow-growing microbial communities arises from thermodynamic constraints
  29. Complementary resource preferences spontaneously emerge in diauxic microbial communities
  30. Stochastic social behavior coupled to COVID-19 dynamics leads to waves, plateaus, and an endemic state
  31. Mitigation of SARS-CoV-2 Transmission at a Large Public University
  32. Time-dependent heterogeneity leads to transient suppression of the COVID-19 epidemic, not herd immunity
  33. Complementary resource preferences spontaneously emerge in diauxic microbial communities
  34. Ecology-guided prediction of cross-feeding interactions in the human gut microbiome
  35. Reduction of chaos in molecular sequences at the Origin of Life
  36. Stochastic social behavior coupled to COVID-19 dynamics leads to waves, plateaus and an endemic state
  37. Modeling COVID-19 Dynamics in Illinois under Nonpharmaceutical Interventions
  38. The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification
  39. Transforming the Language of Life
  40. Entry screening and multi-layer mitigation of COVID-19 cases for a safe university reopening
  41. Ligation of random oligomers leads to emergence of autocatalytic sequence network
  42. Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence
  43. Persistent heterogeneity not short-term overdispersion determines herd immunity to COVID-19
  44. Projections and early-warning signals of a second wave of the COVID-19 epidemic in Illinois
  45. Ecology-guided prediction of cross-feeding interactions in the human gut microbiome
  46. Transforming the Language of Life: Transformer Neural Networks for Protein Prediction Tasks
  47. Ecology-guided prediction of cross-feeding interactions in the human gut microbiome
  48. Modeling COVID-19 dynamics in Illinois under non-pharmaceutical interventions
  49. Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations
  50. Window of Opportunity for Mitigation to Prevent Overflow of ICU capacity in Chicago by COVID-19
  51. Evidence for a multi-level trophic organization of the human gut microbiome
  52. Multistability and regime shifts in microbial communities explained by competition for essential nutrients
  53. The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification
  54. Regime Shifts in a Phage-Bacterium Ecosystem and Strategies for Its Control
  55. Evidence for a multi-level trophic organization of the human gut microbiome
  56. Phages associated with horses provide new insights into the dominance of lateral gene transfer in virulent bacteriophages evolution in natural systems
  57. Predicting tumor cell line response to drug pairs with deep learning
  58. Alternative stable states in a model of microbial community limited by multiple essential nutrients
  59. Onset of natural selection in populations of autocatalytic heteropolymers
  60. Phase transitions in social networks inspired by the Schelling model
  61. Hitchhiking, collapse and contingency in phage infections of migrating bacterial populations
  62. Multiple stable states in microbial communities explained by the stable marriage problem
  63. KBase: The United States Department of Energy Systems Biology Knowledgebase
  64. Diversity, Stability, and Reproducibility in Stochastically Assembled Microbial Ecosystems
  65. Multiple stable states in microbial communities explained by the stable marriage problem
  66. Diversity, stability, and reproducibility in stochastically assembled microbial ecosystems
  67. Onset of natural selection in auto-catalytic heteropolymers
  68. Severe population collapses and species extinctions in multihost epidemic dynamics
  69. Recombination-Driven Genome Evolution and Stability of Bacterial Species
  70. Family-specific scaling laws in bacterial genomes
  71. Severe population collapses and species extinctions in multi-host epidemic dynamics
  72. Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems
  73. Pan- and core- network analysis of co-expression genes in a model plant
  74. DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks
  75. Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis
  76. Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis
  77. Pan- and core- network analysis of co-expression genes in a model plant
  78. Diversity Waves in Collapse-Driven Population Dynamics
  79. Spontaneous emergence of autocatalytic information-coding polymers
  80. Diversity waves in collapse-driven population dynamics
  81. Recombinant transfer in the basic genome of Escherichia coli
  82. Well-temperate phage: optimal bet-hedging against local environmental collapses
  83. Transcriptional Responses to Sucrose Mimic the Plant-Associated Life Style of the Plant Growth Promoting Endophyte Enterobacter sp. 638
  84. Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between Arabidopsis and Poplar
  85. Evolutionary Capacitance and Control of Protein Stability in Protein-Protein Interaction Networks
  86. Universal distribution of component frequencies in biological and technological systems
  87. Joint scaling laws in functional and evolutionary categories in prokaryotic genomes
  88. A Toolbox Model of Evolution of Metabolic Pathways on Networks of Arbitrary Topology
  89. Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions
  90. Understanding the Differences between Genome Sequences of Escherichia coli B Strains REL606 and BL21(DE3) and Comparison of the E. coli B and K-12 Genomes
  91. Power laws in chess
  92. Toolbox model of evolution of prokaryotic metabolic networks and their regulation
  93. Fluctuations in Mass-Action Equilibrium of Protein Binding Networks
  94. Promise and Pitfalls of Extending Google's PageRank Algorithm to Citation Networks
  95. Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks
  96. Constraints imposed by non-functional protein–protein interactions on gene expression and proteome size
  97. Algorithmic Basis for Pathway Visualization
  98. Propagation of Concentration Perturbations in Equilibrium Protein Binding Networks
  99. Topological and Dynamical Properties of Protein Interaction Networks
  100. Propagation of large concentration changes in reversible protein-binding networks
  101. Spreading out of perturbations in reversible reaction networks
  102. Ranking scientific publications using a model of network traffic
  103. UV-Induced Mutagenesis in Escherichia coli SOS Response: A Quantitative Model
  104. Better by half
  105. Exploring an opinion network for taste prediction: An empirical study
  106. Finding scientific gems with Google’s PageRank algorithm
  107. Optimal ranking in networks with community structure
  108. Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins
  109. Automatic pathway building in biological association networks
  110. Computational architecture of the yeast regulatory network
  111. Binding properties and evolution of homodimers in protein-protein interaction networks
  112. UV-induced mutagenesis in Escherichia coli SOS response: A quantitative model
  113. Diffusion on complex networks: a way to probe their large-scale topological structures
  114. Hierarchy Measures in Complex Networks
  115. The conundrum of stock versus bond prices
  116. Detection of topological patterns in complex networks: correlation profile of the internet
  117. Detection of Topological Patterns in Protein Networks
  118. DOES THE PRICE MULTIPLIER EFFECT ALSO HOLD FOR STOCKS?
  119. Modularity and Extreme Edges of the Internet
  120. Protein interaction networks beyond artifacts
  121. Specificity and Stability in Topology of Protein Networks
  122. Measures of globalization based on cross-correlations of world financial indices
  123. Extracting Hidden Information from Knowledge Networks
  124. Price fluctuations from the order book perspective—empirical facts and a simple model
  125. Quantum and classical dynamics in mixed-spin one-dimensional antiferromagnets
  126. Exact solution of a stochastic directed sandpile model
  127. Measures of Globalization Based on Cross-Correlations of World Financial Indices
  128. Energy Separation of Single-Particle and Continuum States in anS=1/2Weakly Coupled Chains Antiferromagnet
  129. Role of single-ion excitations in the mixed-spin quasi-one-dimensional quantum antiferromagnetNd2BaNiO5
  130. Simple model of a limit order-driven market
  131. Simple Model of a Limit Order-Driven Market
  132. Infrared Studies of the Onset of Conductivity in Ultrathin Pb Films
  133. 1/fNoise in Bak-Tang-Wiesenfeld Models on Narrow Stripes
  134. BaCu2Si2O7: A quasi-one-dimensionalS=1/2antiferromagnetic chain system
  135. Magnetic anisotropy and low-energy spin waves in the Dzyaloshinskii-Moriya spiral magnetBa2CuGe2O7
  136. Probability distribution of drawdowns in risky investments
  137. Experimental Evidence for Kaplan–Shekhtman–Entin-Wohlman–Aharony Interactions inBa2CuGe2O7
  138. Critical exponents of the anisotropic Bak-Sneppen model
  139. Magnetic ordering, spin waves, and Haldane-gap excitations in(NdxY1−x)2BaNiO5linear-chain mixed-spin antiferromagnets
  140. Optimal Investment Strategy for Risky Assets
  141. Universal Behavior of One-Dimensional Gapped Antiferromagnets in a Staggered Magnetic Field
  142. Comment on “Role of Intermittency in Urban Development: A Model of Large-Scale City Formation”
  143. Dynamical optimization theory of a diversified portfolio
  144. Experimental Measurement of the Staggered Magnetization Curve for a Haldane Spin Chain
  145. Expansion Around the Mean-Field Solution of the Bak-Sneppen Model
  146. Field-induced incommensurate-to-commensurate transition inBa2CuGe2O7
  147. Coexistence of Haldane-gap excitations and long-range antiferromagnetic order in mixed-spin nickelatesR2BaNiO5
  148. Square-lattice spiral magnetBa2CuGe2O7in an in-plane magnetic field
  149. Field-Induced Commensurate-Incommensurate Phase Transition in a Dzyaloshinskii-Moriya Spiral Antiferromagnet
  150. Infinite Series of Exact Equations in the Bak-Sneppen Model of Biological Evolution
  151. Avalanche dynamics in evolution, growth, and depinning models
  152. Self-organized critical directed percolation
  153. Exactly Solved Model of Self-Organized Criticality
  154. Laws for Stationary States in Systems with Extremal Dynamics
  155. Time Directed Avalanches in Invasion Models
  156. Avalanches and1fNoise in Evolution and Growth Models
  157. Scaling theory of depinning in the Sneppen model
  158. Field Theory for a Model of Self-Organized Criticality
  159. Correlations, mean-field properties, and scaling of a one-dimensional sandpile model
  160. The First Critical Field and Locking-Unlocking Phase Transition in Layered Superconductors