Network Biology 2016
2016-04-11..2016-04-15
Berkeley, United States
[From Algorithms to Discovery in Genome-Scale Biology and Medicine 2022, Computational Cancer Biology 2016, Computational Challenges in Very Large-Scale 'Omics', Statistics in the Big Data Era 2022, New Directions in Probabilistic Models of Evolution, Epidemics and Information Diffusion (Simons Institute, 2022)]
| title | author | length |
|---|---|---|
| Using Molecular Networks to Seed Predictive Hierarchies of Cell Systems | Trey Ideker | 01h 11m |
Builds a data-driven hierarchy from integrated yeast networks (protein, genetic, co-expression) using CLIXO/clique-extracted ontologies and ontology alignment… | ||
| Uncertainty in Biological Networks; Challenges and Opportunities | Tamer Kahveci | 31m |
Proposes representing uncertain interactions with probability-generating polynomials so coefficients give exact degree and joint-degree distributions (no… | ||
| Diffusion-Based Metrics for Biological Network Analysis | Lenore Cowen | 34m |
Defines diffusion state distance as the L1 norm of difference between expected visit-count vectors from K-step random walks (converging as K→∞ and computable… | ||
| Sampling the Low End of Affinity | Marcus Noyes | 28m |
A bacterial omega-based two-hybrid is combined with a HIS3 selectable + GFP scalable reporter so selections (10^9 transformation efficiency) enrich… | ||
| Systematic Functional Annotation of the 2016 Yeast Genetic Interaction Network | Anastasia Baryshnikova | 34m |
Introduces the SAFE method that turns the 2016 yeast genetic interaction similarity network into a spatial analysis of functional enrichment by defining… | ||
| Pathways, Centrality, and Regulation in Developmental Disorders | Donna Slonim | 34m |
Defines pathway centrality as all-pairs shortest-path betweenness from GWAS/disease genes to differentially expressed genes on PPI and directed regulatory… | ||
| On Beyond Genome: Opportunities and Challenges Using the Other Omics for Precision Medicine | Ernest Fraenkel | 36m |
Combines RNA-seq, ChIP-seq, phosphoproteomics and targeted/untargeted mass spec into a merged interactome of ~40,000 nodes and >1,000,000 edges, using a… | ||
| Algorithms for Combinatorial Problems Arising in the Analysis of Cancer Mutation Networks | Fabio Vandin | 35m |
Presents concrete algorithms: NOMAS color-coding adapts color-coding to maximize a non‑additive log‑rank survival score and uses permutations on gene labels to… | ||
| Network Analysis of Cancer Mutations | Ben Raphael | 39m |
Presents an algorithmic fix to HotNet that uses asymmetric heat diffusion / lazy random-walk propagation on interaction graphs, followed by thresholding and… | ||
| Fathoming Cancer by Interrogating Integrated Interactomes | Igor Jurisica | 34m |
Integrates diverse omics, interaction assays and tissue annotation into a network resource with 18,000 proteins and ~800,000 edges and flags prediction… | ||
| Network Data Integration Enables Precision Medicine | Natasa Przulj | 33m |
Uses semi supervised non negative matrix tri factorization with graph Laplacian regularizers and multiplicative update rules to fuse networks of genes GO terms… | ||
| Transcriptional Enhancers - Looking out for the Genes and Each Other | Sridhar Hannenhalli | 35m |
A coupled hierarchical Bayesian model integrates epigenomic enhancer priors and enhancer–gene linking features to fine-map eQTLs in ~300 human hearts… | ||
| Dynamics of 3D Enhancer-Gene Associations Across Diverse Human Cell Types and Tissues | Anshul Kundaje | 37m |
A hierarchical probabilistic mixed‑membership model links chromatin and expression across 127 Roadmap+ENCODE cell types to map enhancers to genes. The pipeline… | ||
| Profiling Cell/Tissue Specific Gene Regulatory Networks | Louxin Zhang | 25m |
Analyzes 41 cell-specific TF regulatory networks (from a 2012 dataset) with ~475 TFs and ~1,100 predicted interactions each, finds hierarchical layout with… | ||
| Variation of Regulatory Networks Across Organisms | Mona Singh | 44m |
Comparative analysis of 12 Drosophila genomes (50 My divergence) inspects 121 ortholog C2H2 zinc fingers using structural positions and Marcus’s bacterial… | ||
| Spatial Gene Expression Patterns in Drosophila | Bin Yu | 31m |
A reproducible pipeline decomposes spatial Drosophila embryo expression (about 1 TB, 405 genes sampled into 405 superpixels) with stability-driven non-negative… | ||
| Network Perspective on Expression Changes and Expression Noise in D. melanogaster Chromosomal Deleti | Teresa Przytycka | 32m |
Teresa Przytycka, National Institutes of Health
Network Biology
https://simons.berkeley.edu/talks/teresa-przytycka-04-13-16 | ||
| Cross-Species Interactome Mapping Reveals Network Evolution Principles from Yeasts to Human | Haiyuan Yu | 39m |
Built a comprehensive fission yeast binary interactome by screening 75 million pairs (5,000 × 5,000 × 3) and reporting about 2,300 interactions across 1,300… | ||
| Moving Beyond Local Patterns: New Ways to Reason about Biological Network Comparisons | Ben Hescott | 34m |
Method embeds each network by measuring diffusion-based distances to a selected set of landmarks (usually one-to-one homologs) and compares nodes in a 200–500… | ||
| Data Driven "Pathway" Analysis with ADAGE | Casey Greene | 35m |
An unsupervised denoising autoencoder approach called ADAGE mines noisy public expression compendia to recover pathway- and gene‑level signals without prior… | ||
| Synthesis, Simplification and Analysis of Biological Networks Using Higher Order Topological Connect | Bhaskar DasGupta | 32m |
Describes three concrete methods and results: using modular response analysis reduced to a set multicover reduction to choose minimal perturbation experiments… | ||
| Network Propagation as a Tool for Deciphering Disease Mechanisms | Roded Sharan | 44m |
Per-sample binary mutation and differential-expression calls are propagated across a 150,000‑edge HIPPI network (random walk with restart) to create propagated… | ||
| Dynamic and Integrative Biological Network Research of Aging | Tijana Milenkovic | 32m |
Combines static PPI (HPRD and binary) with age-resolved expression to build 37 age-specific PPI networks, computes seven centralities per gene and flags… | ||
| Efficiently Enumerating All Connected Induced Subgraphs of a Large Molecular Network | Mehmet Koyuturk | 24m |
Algorithm enumerates every connected induced subgraph on graphs with thousands of nodes and tens of thousands of edges by using anchor vertices and a hybrid… | ||
| Identifying Disease Mechanisms Using Gene Networks as Priors | Anna Goldberg | 39m |
A probabilistic graphical model combines per-variant harmfulness priors, aggregated coding scores and gene-level expression aberration scores, then ties genes… | ||
| Simple Models and Exact Algorithms for Computing Network Modules | Gunnar Klau | 31m |
Presents a sparse pairwise alignment that restricts each node to a candidate set and encodes edge conservation as a quadratic objective, solved by Lagrangian… | ||
| Local Similarity Analysis (LSA) of Time Series Data and Applications to Metagenomics | Fengzhu Sun | 33m |
Method detects short, time-local and time-delayed associations between OTU abundance series that Pearson correlation misses, maximizing a local similarity… | ||
| Module Discovery in 3-way Data | Ron Shamir | 34m |
Probabilistic model for three-way data (subjects × rows × time) that finds a core gene/parcel set plus subject-specific rows and subject-specific time… | ||
| nothing matches | ||