10/01: Jackfin KC, Updates on Android app development
09/09: [Special Seminar] Ms. Miao He from Tokyo Metropolitan University, Syntrophic Association Between Purple Photosynthetic Bacteria and Tetrathionate-Reducing Bacteria
08/16: [Special Seminar] Dr. Mayumi Seto from Nara Women's University, Prediction of microbial redox functions based on thermodynamics and causal inference
08/12-16: Song Lab - Bioinformatics and Modeling Workshop (SL-BMW) led by Hugh McCullough
07/09: Sanjog Kharel, Modelling microbial dynamics in deep subsurface via their energetics
07/03: Yoonmi Choi, Current Status of Plant Modeling: Approaches and Insights
06/25: Insoo Jeon, Plant-driven assembly of disease-suppressive soil microbiomes
06/18: Steve Zhang and Mahsa Mohammadi, ASM highlights
06/06: Steve Zhang and Mahsa Mohammadi, ASM dry run
05/21: Manokaran Veeramani, Bioavailable OM selection to improve predictions of aerobic respiration in river corridors
05/14: Sanjog Kharel, Yoonmi Choi, and Mahsa Mohammadi, BSEN 951 Term Project Presentations
05/07: Manokaran Veeramani, Computational inference of spatial microbial interactions from microscopic images
04/30: Steve Zhang, Building Metabolite-Enzyme Networks using edgeR and NetCom: Functional Enrichment in RSAX and WSAX
04/23: Mahsa Mohammadi, The Impact of Red and White Sorghum Arabinoxylans on Human Gut Microbiota Interactions
04/09: Aimee Kessell, Genome-scale network modeling of chitin-degrading microbial communities and their isolates (thesis defense)
03/26: Aimee Kessell, Genome-scale network modeling of chitin-degrading microbial communities and their isolates (presentation to the Soil Microbiome SFA at PNNL, dry run #2)
03/19: Aimee Kessell, Genome-scale network modeling of chitin-degrading microbial communities and their isolates (dry run #1)
02/27: Sanjog Kharel, Chemolithotrophs in deep subsurface
02/13: Hugh McCullough, Redox Homeostasis and Potential Indicators of Oxidative Stress in Omics Data
02/06: Mahsa Mohammadi, Network-based analysis of metagenomics data
01/30: Steve Zhang, Update: Community Flux Coupling Analysis in Unicyanobacterial Communities
01/23: Kiera Chan, Novel Eigenmode-Based Feature Engineering for Efficient and Interpretable Image Classification: Application to Handwritten Digits
01/10: Sanjog Kharel, Lambda Model for Microbial Growth (2): Identification of bioavailable OM
2023
12/19: Andrea Mikulasova, Flux Balance Analysis: Everything I didn’t know
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
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?
09/26: Hugh McCullough, Intersections of reaction activity from model predictions and omics data
09/19: 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
07/17: Aimee Kessell, Impacts of Bioenergetic Costs of Chitin Decomposition on Degrader Metabolism and Their Interactions with Cheaters
07/03: Huisun Eom, Data-Driven Modeling using SINDy: Application to Biological data and Education-related Data
06/26: Soo Park, Differential response of nitrate-reducing synthetic communities to varying carbon-to-nitrogen ratio
06/05: [Special Seminar] Dr. Sridharakumar Narasimhan at IIT Madras, A Priori Parameter Identifiability - Impact of Measurements in Complex Reaction Networks
05/29: All, 2023 Summer and Beyond
05/22: Manokaran Veeramani, Stochastic simulations for modeling chemical reactions (II)
05/15: Ayeon Park, App development for modeling and simulation of interactions between microbial populations
05/08: Manokaran Veeramani, Stochastic simulations for modeling chemical reactions (I)
05/01: Mahsa Mohammadi, Comparative Study of the Effects of Red and White Sorghum Arabinoxylans on Human Gut Microbiota: Data-Driven Approach
04/24: Steve Zhang, Pathway and Flux Coupling Analysis in Unicyanobacterial Communities
04/10: Hugh McCullough, Structure of Fecal Microbial Communities under Varying Carbohydrate Compositions and Antibiotic Perturbation
04/03: Aimee Kessell, Flux Coupling Analysis – Existing algorithms and new strategies
03/27: Naeun Lee, Metabolic Network Modeling to Unravel the Impact of Copper Deficiency and High-fat Diet on Liver Metabolism
03/20: Firnaaz Ahamed, Coupled flux balance analysis and reactive transport modeling using machine learning
02/27: Soo Park, Changes of N cycling synthetic microbial communities under varying C/N ratios
02/13: Manokaran Veeramani, Modeling of context-dependent microbial interactions in biopolymer degradation networks
02/06: Soo Park, Tutorial: Bipartite graphs using NetworkX and Gephi & Mapping genes onto KEGG pathway using KEGG Color Mapper
01/23: Firnaaz Ahamed, What are the major chemical traits that govern the bioavailability of organic matters in river corridors?
01/09: Kiera Chan, Coupling the Cybernetic Modeling with Flux Balance Analysis for Dynamic Simulation of Overflow Metabolism in Escherichia coli
2022
12/21: Soo Park, C/N ratio of substrate drives the structure of microbial communities in soil
12/12: Mahsa Mohammadi, A brief review of network analysis methods for studying microbial communities
11/28: Hugh McCullough, Media carbohydrate composition’s potential Influence on variability of community assembly and peptide utilization
11/07: Steve Zhang, Flux coupling analysis: Methods and applications
10/31: Aimee Kessell, Constructing a binary metabolic network model to more accurately represent consortium growth on chitin, and its monomer, NAG
10/03: Naeun Lee, DEG-integrated modeling to increase consistency between gene expression data and flux distribution
09/19: Meeting with Dr. Shin Haruta from Tokyo Metropolitan University
08/22: Firnaaz Ahamed, Data-driven optimization allows identification of organic matters governing microbial respiration in river corridors
08/08: Hugh McCullough, Community simplification in vitro: enrichment cultures trend from stochastic to deterministic effects
[Hereafter, every other Monday]
07/22: Steve Zhang, Microbial Division of Labor in Polysaccharide-Degrading Communities
07/15: Aimee Kessell, Omics inclusion for an improved model of a chitin-degrading binary consortium
01/07: Steve Zhang, Tutorial session: Flux balance and variance analysis using CPLEX in Python
2021
12/17: Michael Israel, Cybernetic Modeling Ⅱ & Steve Zhang, Flux Balance and Variance Analysis with CPLEX in Python
12/03: Aimee Kessell, TBA
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
10/15: 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
07/30: Aimee Kessell, dry-run MPA presentation
07/23: Naeun Lee, dry-run MPA presentation
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
06/11: Hugh McCullough, Considerations for experimental models to improve culture of microbial communities
06/01-02: [Hands-on Training] Dr. 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