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Integrated Protein Interaction Networks for 11 Microbes [chapter]

Balaji S. Srinivasan, Antal F. Novak, Jason A. Flannick, Serafim Batzoglou, Harley H. McAdams
2006 Lecture Notes in Computer Science  
We have combined four different types of functional genomic data to create high coverage protein interaction networks for 11 microbes.  ...  technique which produces pairwise measures of protein interaction.  ...  Acknowledgments We thank Lucy Shapiro, Roy Welch, and Arend Sidow for helpful discussions.  ... 
doi:10.1007/11732990_1 fatcat:samggbrlrzem7b2w4mynmenaye

MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome–Host Interactions

Tahila Andrighetti, Balazs Bohar, Ney Lemke, Padhmanand Sudhakar, Tamas Korcsmaros
2020 Cells  
Here, we present MicrobioLink, a computational pipeline to integrate predicted interactions between microbial and host proteins together with host molecular networks.  ...  Despite the biological significance of microbe–host interactions, there is a big gap in understanding the downstream effects of these interactions on host processes.  ...  MicrobioLink integrates microbiome-host protein-protein interaction predictions with network diffusion to infer signaling networks which capture the systemic effects of microbial proteins on host processes  ... 
doi:10.3390/cells9051278 pmid:32455748 pmcid:PMC7291277 fatcat:m5dqzqndbbafjnkp527dvpdurm

Small Molecule Modulation of Microbiome Ecosystem: A Systems Pharmacology Perspective [article]

Qiao Liu, Bohyun Lee, Lei Xie
2020 bioRxiv   pre-print
Integrating microbiome data with chemical genomics and other biological information enables us to delineate the landscape for the small molecule modulation of the human microbiome network.  ...  In this paper, we construct a disease-centric signed microbe-microbe interaction network using metabolite information of microbes and curated microbe effects on human health from published work.  ...  The microbe 255 effects on human health are also integrated into an interaction network.  ... 
doi:10.1101/2020.03.23.003285 fatcat:vcgx3do6xzhe3ow7clsw7gpaty

MicrobioLink: An integrated computational pipeline to infer functional effects of microbiome-host interactions [article]

Tahila Andrighetti, Leila Gul, Tamas Korcsmaros, Padhmanand Sudhakar
2019 bioRxiv   pre-print
Here, we present MicrobioLink, a computational pipeline to integrate predicted interactions between microbial and host proteins with host molecular networks.  ...  With MicrobioLink users can analyse how microbial proteins in a certain context are influencing cellular processes by interacting with host proteins and affecting downstream pathways, regulating gene expression  ...  MicrobioLink integrates microbiome-host protein-protein interaction predictions with network diffusion to infer signaling networks which capture the systemic effects of microbial proteins on host processes  ... 
doi:10.1101/837062 fatcat:tovwjwlmlng2pncu3z3tpqapou

Predicting Drugs for COVID-19/SARS-CoV-2 via Heterogeneous Graph Attention Networks

Yahui Long, Yu Zhang, Min Wu, Shaoliang Peng, Chee Keong Kwoh, Jiawei Luo, Xiaoli Li
2020 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
Identifying drug-virus associations can not only provide insights into the understanding of drug-virus interaction mechanism, but also guide and facilitate the screening of compound candidates for antiviral  ...  In this work, we propose a novel framework of Heterogeneous Graph Attention Networks for Drug-Virus Association predictions, named HGATDVA.  ...  We further construct a drug-host-virus heterogeneous network named Net2 by integrating drug-target interactions (DTIs) with virus-host (human) protein-protein interactions (PPIs).  ... 
doi:10.1109/bibm49941.2020.9313472 fatcat:dv5e72wxnbecxnuqofm7ig47ti

Metabolic networks of microbial systems

Sumana Bhattacharya, Subhra Chakrabarti, Amiya Nayak, Sanjoy K Bhattacharya
2003 Microbial Cell Factories  
With the advent of neo-integrative proteomic approaches the understanding of integration of metabolic and protein-protein interaction networks have began.  ...  In this article we review the methods employed to determine the protein-protein interaction and their integration to define metabolite networks.  ...  Metabolic and protein-protein interaction network The cellular processes in a microorganism are seamlessly integrated through a complex network of constituent components and reactions.  ... 
pmid:12740044 pmcid:PMC155636 fatcat:6g4fklgusnhbhpnyypztzynxha

Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes

Patrick A. Leggieri, Yiyi Liu, Madeline Hayes, Bryce Connors, Susanna Seppälä, Michelle A. O'Malley, Ophelia S. Venturelli
2021 Annual Review of Biomedical Engineering  
and modeling approaches can be integrated to address these gaps.  ...  Throughout the review,we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics  ...  and exchanged to form an integrated community metabolic network.  ... 
doi:10.1146/annurev-bioeng-082120-022836 pmid:33781078 pmcid:PMC8277735 fatcat:gja3drhb2zebfpvpz6epgs5piu

Disentangling leaf-microbiome interactions in Arabidopsis thaliana by network mapping [article]

Kaihang Li, Kexin Cheng, Haochen Wang, Qi Zhang, Yan Yang, Yi Jin, Xiaoqing He, Rongling Wu
2022 bioRxiv   pre-print
Many genome-wide association studies (GWAS) have begun to map leaf microbes, but few has systematically characterized the genetics of how microbes act and interact.  ...  Many genome-wide association studies (GWAS) have begun to map leaf microbes, but few has systematically characterized the genetics of how microbes act and interact.  ...  Bergelson for supplying their leaf Arabidopsis microbiome and SNP data to us.  ... 
doi:10.1101/2022.04.05.487248 fatcat:2gaphx33nnbffojkbnxk3ieyee

Metabolome–Microbiome Crosstalk and Human Disease

Kathleen A. Lee-Sarwar, Jessica Lasky-Su, Rachel S. Kelly, Augusto A. Litonjua, Scott T. Weiss
2020 Metabolites  
Methods for integrative analysis of these "omics" are under active investigation and we discuss the advances and challenges in the combined use of metabolomics and microbiome data.  ...  Mechanisms whereby the microbes residing in the human body interact with metabolites to impact disease risk are beginning to be elucidated, and discoveries in this area will likely be harnessed to develop  ...  However, integration of human microbiome and metabolome data is challenging for several reasons [11] .  ... 
doi:10.3390/metabo10050181 pmid:32369899 pmcid:PMC7281736 fatcat:mkoqjsidovcvhfzhgcecueowpy

Toward design-based engineering of industrial microbes

Keith EJ Tyo, Kanokarn Kocharin, Jens Nielsen
2010 Current Opinion in Microbiology  
Genome scale metabolic models, new tools for controlling expression, and integrated -omics analysis are described as key contributors in moving the field toward design-based engineering.  ...  Engineering industrial microbes has been hampered by incomplete knowledge of cell biology.  ...  Protein-protein interaction networks provide a scaffold for models that describe non-metabolic processes in the cell and are currently a useful resource for data analysis (described below).  ... 
doi:10.1016/j.mib.2010.02.001 pmid:20226723 pmcid:PMC2885540 fatcat:h527tb74breg7fkz2id2mwk47u

Systems biology in inflammatory bowel diseases

Christos Polytarchou, Georgios Koukos, Dimitrios Iliopoulos
2014 Current Opinion in Gastroenterology  
The future IBD therapeutics should be developed on the basis of targeting the central hubs in the IBD network.  ...  Novel computational methodologies have been developed aiming to integrate high-throughput molecular data.  ...  This will be realized by integrating the molecular networks in each of the gut components (cells, microbes) and construct a larger network which will reveal interactions between these different components  ... 
doi:10.1097/mog.0000000000000081 pmid:24837229 fatcat:nanoxqetqrga7egdel45dmcgv4

Systems biology and metagenomics: a showcase of Chinese bioinformatics researchers and their work

DongXiao Zhu, Zhaohui S. Qin
2014 Science China Life Sciences  
In their approach, they used shortest-path algorithm to prioritize the disease gene in the protein-protein interaction network by integrating the semantic similarity of GO annotations.  ...  [7] proposed a computational approach to investigate the microbial interaction networks existing among the microbes.  ... 
doi:10.1007/s11427-014-4755-6 pmid:25326071 fatcat:b7ihivc6lnhszbqbruhqimw3wu

Autonomous and Assisted Control for Synthetic Microbiology

Alvaro Banderas, Matthias Le Bec, Céline Cordier, Pascal Hersen
2020 International Journal of Molecular Sciences  
A "hybrid biology" approach, where robust synthetic microbes interact with natural consortia and—additionally—with external computers, could become a useful tool for health and environmental applications  ...  This is especially true for intercellular signaling circuits for synthetic consortia, where robustness is highly desirable, but its mechanisms remain unclear.  ...  Acknowledgments: We thank Ariel Lindner and Sylvain Pouzet for helpful discussions. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms21239223 pmid:33287299 fatcat:rciwhexyvzgnlacwaplrqn2eya

Towards an Integrative Understanding of Diet–Host–Gut Microbiome Interactions

Mark N. Read, Andrew J. Holmes
2017 Frontiers in Immunology  
We posit that integrative approaches to teasing apart diet-microbe-host interactions will help bridge between experimental data sets and conceptual models and will be of value in formulating predictive  ...  We highlight how "units of response," characterizations of similarly behaving microbes, do not correlate consistently with microbial sequence relatedness, raising a challenge for relating high-throughput  ...  They constitute a carbohydrate and protein source to intestinal microbes, structurally distinct from dietary sources.  ... 
doi:10.3389/fimmu.2017.00538 pmid:28533782 pmcid:PMC5421151 fatcat:xr5vrkx6ondopkwlzy6hfyg4qa

Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview

Partho Sen, Matej Orešič
2019 Metabolites  
GSMM can, for example, be applied to estimate the metabolic capabilities of microbes in the gut.  ...  Genome-scale metabolic modeling (GSMM) is an emerging approach that has been increasingly applied to infer diet–microbiome, microbemicrobe and host–microbe interactions under physiological conditions.  ...  Acknowledgments: We thank to Alex Dickens and Santosh Lamichhane for helpful scientific discussions. We also  ... 
doi:10.3390/metabo9020022 pmid:30695998 pmcid:PMC6410263 fatcat:3xgsy2jrxfe2ld4uhubvpfrefa
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