Network-Based Discovery: Seeing the Forest for the Trees - Adventures with 82,000 Phenotypes

Published on 2016-09-211021 Views

Biological organisms are complex systems that are composed of pleiotropic functional networks of interacting molecules and macro-molecules. Complex phenotypes are the result of orchestrated, hierarchi

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Presentation

Network-Based Discovery: Seeing the Forest for the Trees00:00

Experimental Data Types06:13:25

Results43:37:55

Populus: Linking genes to complex phenotypes49:29:12

Vectors across Two Different Types of Matrices61:31:41

Manhattan Plot65:21:59

Populus: Linking genes to complex phenotypes75:42:58

Network Theory: The Practical79:56:42

Co-evolution Networks: SNP Correlations99:16:59

Big data and high performance computing reveals the underlying biological signatures - 1112:40:59

Big data and high performance computing reveals the underlying biological signatures - 2121:00:17

Big data and high performance computing reveals the underlying biological signatures - 3125:41:22

Targets of Interest: Gene Co-evolution Networks144:04:04

Gene Co-evolution Networks150:07:52

Big data and high performance computing reveals the underlying biological signatures - 4171:18:19

Infrastructure181:21:43

GWAS Networks207:01:33

The use of GWAS networks217:00:12

Preliminary: GWAS-Profile Correlation221:44:37

GWAS-Profile Correlation Methods - 1227:17:28

GWAS-Profile Correlation Methods - 2231:55:22

GWAS-Profile Correlation Methods - 3234:12:40

GWAS-Profile Correlation Methods - 4234:27:31

GWAS-Profile Correlation Methods - 5235:48:26

GWAS-Profile Correlation Methods - 6235:55:15

GWAS-Profile Correlation Methods - 7235:59:08

GWAS-Profile Correlation Methods - 8236:06:01

GWAS Profile Network - 1236:18:19

GWAS Profile Network - 2242:23:24

GWAS Profile Network - 3247:34:06

GWAS Profile Network - 4250:43:15

GWAS Profile Network - 5251:33:39

GWAS Profile Network - 6258:21:32

GWAS Profile Network - 7259:30:13

Lignin Focused Network281:12:55

Seed Subnetwork Creation - 1291:15:11

Seed Subnetwork Creation - 2300:58:34

Seed Subnetwork Creation - 3305:39:46

Seed Subnetwork Creation - 4306:38:56

Seed Subnetwork Creation - 5306:45:02

Seed Subnetwork Creation - 6306:54:16

Seed Subnetwork Creation - 7307:40:09

Seed Subnetwork Creation - 9313:10:56

Seed Subnetwork Creation - 10319:26:00

Seed Subnetwork Creation - 11334:42:28

Seed Subnetwork Creation - 12342:39:43

Seed Subnetwork Creation - 13346:18:07

Seed Subnetwork Creation - 14358:23:03

Seed Subnetwork Creation - 15369:38:32

Seed Subnetwork Creation - 16371:37:38

Seed Subnetwork Creation - 17373:32:39

Seed Subnetwork Creation - 18381:31:56

Seed Subnetwork Creation - 19386:45:32

Seed Subnetwork Creation - 20388:21:49

Seed Subnetwork Creation - 21389:51:02

Seed Subnetwork Creation - 22399:07:09

Seed Subnetwork Creation - 23412:56:30

Seed Subnetwork Creation - 24413:54:47

Seed Subnetwork Creation - 25419:58:15

Seed Subnetwork Creation - 26424:48:06

Seed Subnetwork Creation - 27429:20:40

Seed Subnetwork Creation - 28431:06:00

Seed Subnetwork Creation - 19433:19:21

Seed Subnetwork Creation - 30445:25:55

Seed Subnetwork Creation - 31459:37:24

Seed Subnetwork Creation - 32461:07:22

Seed Subnetwork Creation - 33463:37:59

Seed Subnetwork Creation - 34469:14:40

Gene Projection488:35:34

GAUT Integrated Phenotypes - 1507:41:33

Creating new, expanded hypotheses Galacturonosyltransferase (GAUTs)510:53:47

GAUT Integrated Phenotypes - 2515:09:42

GAUT11 pyMBMS Cluster - 1517:05:36

pyMBMS Annotations522:20:04

GAUT11 pyMBMS Cluster - 2532:05:32

Gene Annotations Associated with pyMBMS Cluster533:56:21

What about our friend DUF1118?542:50:52

GAUT11 pyMBMS Cluster - 3544:12:24

GAUT11 pyMBMS Cluster - 4545:34:46

Plant-Microbial Interfaces - 1553:46:31

Plant-Microbial Interfaces - 2558:12:41

Plant-Microbial Interfaces - 3585:46:39

Testable hypotheses: Putative models unfold - 1594:59:28

Testable hypotheses: Putative models unfold - 2601:23:10

Testable hypotheses: Putative models unfold - 3608:18:09

Background on Viruses612:00:31

Aim 1: Develop tools - 1628:51:40

Aim 1: Develop tools - 2632:27:46

Aim 1: Develop tools - 3638:38:59

Microbes and Viruses Across the GWAS Population - 1648:29:56

Microbes and Viruses Across the GWAS Population - 2658:22:06

Receptor- Centric Network665:52:20

Virus and Bacteria Receptor Intersection670:11:37

Virus and Bacteria Intersection - 1674:44:30

Virus and Bacteria Intersection - 2682:45:40

Virus and Bacteria Intersection - 3688:34:02

Endophytic Microbiome / Viriome Community Structure712:33:06

Focused Integrated Networks719:41:02

Future Work738:29:32

Phenologs - 1742:01:38

Phenologs - 2745:49:00

Phenologs - 3750:25:28

Mining for Phenologous Patterns791:13:28

Neuroblastoma - 1802:55:45

Human: Neuroblastoma Phenotype - 1806:57:41

Human: Neuroblastoma Phenotype - 2808:17:20

Poplar: Growth Phenotypes810:20:03

Poplar: Budflush, Developmental Phenotype811:50:47

Neuroblastoma - 2815:21:41

Questions to explore844:52:39

3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics848:37:56

Scaling up Computational Biology to Address Biological Complexity: High Performance Computing872:21:26

Exascale Computing: 3-way Networks875:54:41

Exascale Computing: 4-way Networks878:47:37

CASBA Platform887:27:05

ORNL Supercomputing900:16:00

System-wide understanding of Complex Biological Systems905:15:23

Acknowledgements - 1911:09:52

Acknowledgements - 2915:16:49

Acknowledgements - 3919:47:12

Funding924:19:16

Expanding925:40:51

Thank You929:07:15