Intellectual Property
Algorithms and Portals
| Name with brief description | Links |
| 1. MINER
An algorithm to map mutations within tumors that causally perturb the regulators to drive downstream changes in disease phenotype. |
Code: https://github.com/baliga-lab/miner2
Documentation: https://baliga-lab.github.io/miner2/ Reference: https://pubmed.ncbi.nlm.nih.gov/34183722/ |
| 2. SYGNAL/gbmSYGNAL
SYGNAL integrates correlative, causal and mechanistic inference approaches into a framework that systematically infers the causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. |
Web: http://glioma.systemsbiology.net/
Code: https://github.com/baliga-lab/sygnal Reference: https://pubmed.ncbi.nlm.nih.gov/27426982/ |
| 3. Multiple Myeloma Network Portal
MM Network Portal is a web portal to explore causal mechanistic regulatory network and programs for multiple myeloma based on the MINER/SYGNAL algorithm. |
Web: https://myeloma.systemsbiology.net
Code: https://github.com/baliga-lab/mmapi Reference: https://pubmed.ncbi.nlm.nih.gov/34183722/ |
| 4. Transcription Factor Binding Site Database (TFBSDB)
A database of transcription factor (TF) to target gene interactions that was constructed to facilitate construction of gene regulatory networks |
Web: http://tfbsdb.systemsbiology.net/ |
| 5. The cancer miRNA regulatory network (CMRN)
The CMRN was constructed by inferring miRNA mediated regulation for 2,240 gene co-expression signatures from 46 cancer transcriptome profiling studies. |
Web: https://cmrn.systemsbiology.net
Code: https://github.com/baliga-lab/Cancer-miRNA-Regulatory-Network Reference: https://pubmed.ncbi.nlm.nih.gov/22745231/ |
| 6. A Framework for Inference of Regulation by miRNAS (FIRM) FIRM integrates three best performing algorithms to infer miRNA mediate regulation from co-expression signatures. | Web: https://cmrn.systemsbiology.net/firm/
Code: https://github.com/baliga-lab/firm2 Reference: https://pubmed.ncbi.nlm.nih.gov/22745231/ |
| 7. miRvestigator
Framework designed to take a list of co-expressed genes as input and will return the most likely regulatory miRNAs. |
Web: https://mirvestigator.systemsbiology.net
Code: https://github.com/baliga-lab/miRvestigator_www Reference: https://pubmed.ncbi.nlm.nih.gov/22745231/ |
| 8. Biclustering algorithms (cMonkey/ cMonkey2) that integrate disaparate multi-omic datasets to discover disease-associated modules of genes that can simultaneously sub-type disease and stratify patients into different risk-groups
· cMonkey: detects putative co-regulated gene groupings by integrating the bi-clustering of gene expression data and various functional associations with the de novo detection of sequence motifs · cMonkey2: is the Python implementation of the cMonkey algorithm based on the original R implementation |
cMonkey:
Web: https://baliga.systemsbiology.net/projects/cmonkey/ Code: https://github.com/baliga-lab/cMonkey1 Reference: https://pubmed.ncbi.nlm.nih.gov/16749936/ cMonkey2: Web: https://baliga.systemsbiology.net/projects/cmonkey2/ Reference: https://pubmed.ncbi.nlm.nih.gov/25873626/ |
| 9. Inferelator
An algorithm for inferring predictive regulatory networks from gene expression data. |
Web: https://baliga.systemsbiology.net/the-inferelator/
Code: https://github.com/baliga-lab/cMonkeyNwInf Reference: https://pubmed.ncbi.nlm.nih.gov/16686963/ |
| 10. EGRIN 2.0
A model that delineates the complex relationship between environment, gene regulation, and phenotype in prokaryotes |
Web: http://egrin2.systemsbiology.net
Code: https://github.com/baliga-lab?&q=egrin Reference: https://pubmed.ncbi.nlm.nih.gov/25028489/ |
| 11. Network Portal
The Network Portal is a database of gene transcription regulatory networks and enables exploration, annotation and comparative analysis. |
Web: http://networks.systemsbiology.net/
Code: https://github.com/baliga-lab/network_portal Reference: https://www.ncbi.nlm.nih.gov/pubmed/24271392 |
| 12. XCures SNO Heatmap
An Interactive web app for exploration of the SYGNAL analysis for 72 GBM patients |
Web: https://parlak.systemsbiology.net/XCures_SNO_Heatmap/ |
| 13. SCCA Myeloma Cohort SYGNAL Analysis
An interactive web app for exploration of SYGNAL analysis for 23 SCCA Myeloma Patients |
Web: https://sturkarslan.shinyapps.io/sygnomics-SCCA/ |
| 14. SYGNOMICS Patient Report Dashboard
An interactive prototype of SYGNOMICS patient dashboard |
Web: https://d1vpx1gh8mupsj.cloudfront.net/index.html |
| 15. SPO Prototype
Initial SPO prototype that was developed in collaboration with software development company, Slalom. |
Web: https://web.staging.sygnomics.net
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Publications
Select papers that explain why we can decipher predictive gene network models for any organism.
- Systems The scale of prediction. Baliga NS. Science. 2008 Jun 6;320(5881):1297-8. doi: 10.1126/science.1159485.
- The role of predictive modelling in rationally re-engineering biological systems. Koide T, Pang WL, Baliga Nat Rev Microbiol. 2009 Apr;7(4):297-305. doi: 10.1038/nrmicro2107.
- Reverse engineering systems models of regulation: discovery, prediction and Ashworth J, Wurtmann EJ, Baliga NS. Curr Opin Biotechnol. 2012 Aug;23(4):598-603. doi: 10.1016/j.copbio.2011.12.005. Review
Select papers describing SYGNAL platform and its applications.
- A Single-Cell Based Precision Medicine Approach Using Glioblastoma Patient-Specific Models. Park, James H., Feroze, A.H., Emerson, S.N., Mihalas, A.B., Keene, C.D., Cimino, P.J., Garcia de Lomana, A.L., Kannan, K., Wu, W.J., Turkarslan, S., Baliga, N.S. NPJ Precision Oncology, vol. 6, no. 1, Aug. 2022, p. 55,
- Genetic program activity delineates risk, relapse, and therapy responsiveness in Multiple Myeloma. Wall MA, Turkarslan S, Wu W, Danziger SA, Reiss DJ, Mason MJ, Dervan AP, Trotter MW, Bassett D, Hershberg RM, García de Lomana A, Ratushny AV, Baliga NS. 2021. NPJ Precision Oncology, vol. 5, no. 1, June 2021, p. 60
- Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis. Plaisier CL, O’Brien S, Bernard B, Reynolds S, Simon Z, Toledo CM, Ding Y, Reiss DJ, Paddison PJ, Baliga Cell Syst. 2016 Aug;3(2):172-86. doi: 10.1016/j.cels.2016.06.006.
Select papers on algorithms developed for network inference:
- Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. Reiss DJ, Baliga NS, Bonneau BMC Bioinformatics. 2006 Jun 2;7:280.
- The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson Genome Biol. 2006;7(5): R36.
- miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome Plaisier CL, Bare JC, Baliga NS. Nucleic Acids Res. 2011 Jul;39(Web Server issue): W125-31. doi: 10.1093/ nar/gkr374.
- Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers. Ashworth J, Bernard B, Reynolds S, Plaisier CL, Shmulevich I, Baliga Nucleic Acids Res. 2014 Dec 1;42(21):12973-83. doi: 10.1093/nar/ gku1031.
- cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. Reiss DJ, Plaisier CL, Wu WJ, Baliga Nucleic Acids Res. 2015 Jul 27;43(13): e87. doi: 10.1093/nar/gkv300
- Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions. Danziger SA, Reiss DJ, Ratushny AV, Smith JJ, Plaisier CL, Aitchison JD, Baliga BMC Syst Biol. 2015;9 Suppl 2:S1. doi: 10.1186/1752-0509-9-S2-S1.
Select papers on how we do it with examples of applications to microbes and complex human diseases (GBM and MM)
- ·Mathematical Models to Study the Biology of Pathogens and the Infectious Diseases They Cause. Xavier, Joao B., et al. IScience, vol. 25, no. 4, Apr. 2022, p. 104079,
- A Systems-Level Gene Regulatory Network Model for Plasmodium Falciparum. Neal,M., Wei, L., Peterson, E., Arrieta-Ortiz, M.L., Danziger, S.A., Baliga, N.S., Kaushansky, A., Aitchison, J. Nucleic Acids Research, Jan. 2021
- Predictive Regulatory and Metabolic Network Models for Systems Analysis of Clostridioides Difficile. Arrieta-Ortiz, M.L., Immanuel, S.R.C., Turkarslan, S., Wu, W.J., Girinathan, BP., Worley, J.N., DiBenedetto, N., Soutourina, O., Peltier, J., Dupuy, B., Bry, L., Baliga, N.S. Cell Host & Microbe, vol. 29, no. 11, Nov. 2021, pp. 1709-1723.e5
- A system-level model for the microbial regulatory genome. Brooks AN, Reiss DJ, Allard A, Wu WJ, Salvanha DM, Plaisier CL, Chandrasekaran S, Pan M, Kaur A, Baliga Mol Syst Biol. 2014 Jul 15; 10:740. doi: 10.15252/msb.20145160.
- A predictive model for transcriptional control of physiology in a free living cell. Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, Diruggiero J, Johnson CH, Hood L, Baliga Cell. 2007 Dec 28;131(7):1354-65.
- A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Plaisier CL, Pan M, Baliga Genome Res. 2012 Nov;22(11):2302-14. doi: 10.1101/gr.133991.111.
- Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis. Peterson EJ, Ma S, Sherman DR, Baliga Nat Microbiol. 2016 Jun 6;1(8):16078. doi: 10.1038/nmicrobiol.2016.78.
- A high-resolution network model for global gene regulation in Mycobacterium tuberculosis. Peterson EJ, Reiss DJ, Turkarslan S, Minch KJ, Rustad T, Plaisier CL, Longabaugh WJ, Sherman DR, Baliga Nucleic Acids Res. 2014 Oct;42(18):11291-303. doi: 10.1093/nar/gku777.
- A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis. Turkarslan S, Peterson EJ, Rustad TR, Minch KJ, Reiss DJ, Morrison R, Ma S, Price ND, Sherman DR, Baliga Sci Data. 2015 Mar 31;2:150010. doi: 10.1038/ sdata.2015.10.
- Understanding the brain tumor microenvironment: Considerations to applying systems biology and immunotherapy. Juarez TM, Carrillo JA, Achrol AA, Salomon MP, Marzese DM, Park JH, Baliga NS, Kesari S. International Journal of Neurooncology. 2018 Jan 1;1(1):25.