11/28, Manokaran Veeramani, Overview of similarity measures/metrics for comparing spatial data
11/21, Hugh McCullough, Clustering of River Samples by Functional Traits identified by DRAM
11/14, Aimee Kessell, Isolate and Community Model Updates – Improvements and Drawbacks
11/07, No meeting
10/31, Mahsa Mohammadi, Combination of kinetic-based modeling and metabolic network modeling
10/26, Steve Zhang, Combining KIDI with SteadyCom in Modeling Unicyanobacterial Communities
10/19, Sanjog Kharel, Lambda model for microbial growth
10/12, Toko Hisano, How do incomplete denitrifying bacteria survive in nature?
10/03, No meeting
9/26: Hugh McCullough, Intersections of reaction activity from model predictions and omics data
9/19: Aimee Kessell, Predicting flux within a community via SteadyCom
09/12: Manokaran Veeramani, Inference of Spatial Interactions from Long-Term Image Data
09/05: Mahsa Mohammadi, Review of LIMITS algorithm
08/28: Yoan Ghaffar, Residents' impact on the indoor environment; Kiera Chan, Applying Singular Value Decomposition to Extract Shape Features in Handwritten Digits
08/21: Steve Zhang, Modeling of Metabolism and Autotroph-Heterotroph Interactions in UCC-A and UCC-O
08/14: Hugh McCullough, Soil microbiome responses to environmental perturbations
07/24, 07/31, 08/07: No meeting
07/17: Aimee Kessell, Impacts of Bioenergetic Costs of Chitin Decomposition on Degrader Metabolism and Their Interactions with Cheaters
01/07: Steve Zhang, Tutorial session: Flux balance and variance analysis using CPLEX in Python
2021
12/24, 31: No Meeting (Christmas Week)
12/17: Michael Israel, Cybernetic Modeling Ⅱ & Steve Zhang, Flux Balance and Variance Analysis with CPLEX in Python
12/10: No meeting (Canceled)
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 Shah, Tutorial 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 Ahamed, Science 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 Zhang, Pathogen 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 Singh, Understanding 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