Song Group - Group Seminar

Group Seminar

2021

  • 12/25: No Meeting (Christmas Week)
  • 12/17: Hugh McCullough, TBA
  • 12/10: Steve Zhang, TBA 
  • 12/03: Aimee Kessell, TBA
  • 11/26: No meeting (Thanksgiving Break)
  • 11/19: Firnaaz Ahamed, Literature review: Can ensemble modeling improve uncertainties in metabolic network reconstruction?
  • 11/12: Naeun Lee, Identification of impacts by high-fat diet and Cu deficiency via FVA and flux sampling
  • 11/05: Hugh McCullough, AIChE Presentation Practice / Microbiome Meta-Ecosystems and Meta-communities
  • 10/29: Michael Israel, Cybernetic Modeling
  • 10/22: No meeting
  • 10/15: Steve Zhang, FBA
  • 10/08: Aimee Kessell, A Deeper Look into Microbial Cross-Feeding to Expanding the Metabolic Niche of Bacteria
  • 10/01: Firnaaz Ahamed, Predicting organic matter thermodynamics and respiration kinetics via elemental composition of metabolomics data
  • 09/24: Naeun Lee, Modeling of Cu deficiency in the liver with a high-fat diet, and expected changes of enzymes
  • 09/17: Hugh McCullough, Cultivating and Identifying Interactions of Adjacent Bacterial Communities
  • 09/10: Aimee Kessell, Metabolic Network Modeling Helps Determine Interactions In A Complex Polysaccharide-Decomposing Microbial Community
  • 09/03: Firnaaz Ahamed, Metabolic network reconstruction using omics-enabled global gapfilling (OMEGGA) approach
  • 08/27: Naeun Lee, Preprocessing for integration of transcriptomic data into the model & Ten rules for organized paper
  • 08/20: Hugh McCullough, Paper Share: Challenges in microbial network construction and analysis / Bio Image analysis with ilastik
  • 08/13: Ab Rauf Shah, Disentangling soil microbiome functions by Interkingdom Modeling
  • 08/06: No meeting (MPA conference)
  • 07/30: Aimee Kessell, dry-run MPA presentation 
  • 07/23: Naeun Lee, dry-run MPA presentation
  • 07/16: No meeting (Canceled)
  • 07/09: Firnaaz Ahamed, Comparison between variance-based local sensitivity and density-based global sensitivity analysis
  • 07/02: Steve Zhang, Using SINDy and PAWN to Create Equations Predicting the D-Value and Evaluate Sensitivity of Environmental Factors
  • 06/25: Naeun Lee, Omics and metabolic network integration to predict the impacts of Cu limitation on the liver functions and energy metabolism     
  • 06/18: No Meeting (Juneteenth holiday)
  • 06/11: Hugh McCullough, Considerations for experimental models to improve culture of microbial communities
  • 06/01-02: Joon-Yong Lee from PNNL, KBase app development using SDK 
  • 05/21: Ab Rauf ShahTutorial session (II) on "making gap-free genome-scale models"
  • 05/14: Ab Rauf Shah, Tutorial session (I) on "making gap-free genome-scale models"
  • 05/07: All, Summer Plan Sharing 
  • 04/30: Aimee Kessell, Fungal annotation and modeling 
  • 04/23: Firnaaz AhamedScience in PNNL River Corridor SFA
  • 04/16: Ab Rauf Shah, Reconstruction and Analysis of Maize root-specific metabolic models captures the programming of metabolism through multiple root types and developmental stages
  • 04/09: Steve ZhangPathogen Inactivation in Meats
  • 04/02: Naeun Lee, Suggestion of the possibility that SSAO and BMP7 may be associated with Cu-deficiency adaptive response
  • 03/26: Puranjit SinghUnderstanding multiscale model of fungal growth and its regulation (2)
  • 03/19: Puranjit Singh, Understanding multiscale model of fungal growth and its regulation (1)
  • 03/12: Hugh McCullough, Mucins and their role in spatial heterogeneity of gut microbiota
  • 03/05: Aimee Kessell, Science in PNNL Soil Microbiome SFA  
  • 02/26: Firnaaz Ahamed, Modeling microbial competition potentially explains priming effects in soil ecosystem and hyporheic corridor
  • 02/19: Steve Zhang, Using SINDY and sparse regression to predict D- values and parameters
  • 02/12: Naeun Lee, Copper in Lipid Metabolism and Energy Homeostasis & Analysis Liver Transcriptomics Data in Matlab
  • 02/05: Puranjit Singh, Dynamic Flux Balance Analysis
  • 01/29: Hugh McCullough, Inference of microbial interactions from time series data using LIMITS
  • 01/22: Aimee Kessell, Using HCC to solve MATLAB code & Literature Review on Spatial Modeling Technique
  • 01/15: Firnaaz Ahamed, Modelling Consolidated Bioprocessing of Cellulose via Population Balances Coupled with Cybernetic Models
  • 01/08: Hugh McCullough, Microbial Dark Matter; Puranjit Singh, Dynamic Flux Balance Analysis 

2020

  • 12/25: No Meeting (Christmas Week)
  • 12/18: Hyun-Seob SongIssues in Inferring Microbial Correlation Networks from Relative Abundances 
  • 12/11: Hugh McCulloughNetwork Analysis of Fecal Microbial Communities under Differing Carbohydrate Contexts
  • 12/04: Bingjun ZhuMicrobial Models for Food Safety and Security
  • 11/27: No Meeting (Thanksgiving Week)
  • 11/20: Aimee KessellIntegration of Data-driven and FBA for Modeling Context-dependent Interactions
  • 11/13: Puranjit SinghCybernetic Modeling of Microbial Growth Patterns
  • 11/06: JahangeerMicrobial Models for Food Safety and Security
  • 10/30: Bingjun Zhu/Jahangeer,  Microbial Growth Models
  • 10/23: Hyun-Seob Song, Modeling Microbial Intelligence
  • 10/16: Puranjit Singh, What is Flux Balance Analysis?
  • 10/09: Aimee KessellDynamical Flux Balance Analysis for a Binary Model Consortium
  • 10/02: Hugh McCulloughAlternate Sigma Factors and Life Stage Dependency on Microbial Function and Interactions
  • 09/25: JahangeerMetabolomics and Lipidomic Data Integration into Metabolic Network Modeling
  • 09/18: Naeun LeeMetabolic Modeling of Adipose Cell: The Effect of Copper
  • 09/11: Aimee KessellModel Construction for Cellvibrio japonicus and Escherichia coli
  • 09/04: Hugh McCulloughTheoretical Frameworks for Context Dependency
  • 08/31: Aimee KessellMetabolic Modeling of Cellvibrio japonicus and Escherichia coli
  • 08/21: Naeun LeeDiseases Classification through Machine Learning using Human Gut Microbiome Dataset
  • 08/07: Aimee KessellScience Plans and Context-Dependent Dynamics
  • 07/17: Aimee KessellNetwork Reduction Methods
  • 07/03: Hugh McCulloughInteraction Network Inference and Experimental Design
  • 06/26: JahangeerSoil Microbiome Modeling: Multi Omics approach review