NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation
Levy, Roie, Carr, Rogan, Kreimer, Anat, Freilich, Shiri, Borenstein, Elhanan
Published in BMC bioinformatics (17.05.2015)
Published in BMC bioinformatics (17.05.2015)
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Journal Article
large-scale organization of the bacterial network of ecological co-occurrence interactions
Freilich, Shiri, Kreimer, Anat, Meilijson, Isacc, Gophna, Uri, Sharan, Roded, Ruppin, Eytan
Published in Nucleic acids research (01.07.2010)
Published in Nucleic acids research (01.07.2010)
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Journal Article
Competitive and cooperative metabolic interactions in bacterial communities
Freilich, Shiri, Zarecki, Raphy, Eilam, Omer, Segal, Ella Shtifman, Henry, Christopher S, Kupiec, Martin, Gophna, Uri, Sharan, Roded, Ruppin, Eytan
Published in Nature communications (13.12.2011)
Published in Nature communications (13.12.2011)
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Journal Article
Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation
Ofaim, Shany, Zarecki, Raphy, Porob, Seema, Gat, Daniella, Lahav, Tamar, Kashi, Yechezkel, Aly, Radi, Eizenberg, Hanan, Ronen, Zeev, Freilich, Shiri
Published in Scientific reports (03.08.2020)
Published in Scientific reports (03.08.2020)
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Journal Article
Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling
Ruan, Zhepu, Chen, Kai, Cao, Weimiao, Meng, Lei, Yang, Bingang, Xu, Mengjun, Xing, Youwen, Li, Pengfa, Freilich, Shiri, Chen, Chen, Gao, Yanzheng, Jiang, Jiandong, Xu, Xihui
Published in Nature communications (01.06.2024)
Published in Nature communications (01.06.2024)
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Journal Article
Effect of Washing, Waxing and Low-Temperature Storage on the Postharvest Microbiome of Apple
Abdelfattah, Ahmed, Whitehead, Susan R, Macarisin, Dumitru, Liu, Jia, Burchard, Erik, Freilich, Shiri, Dardick, Christopher, Droby, Samir, Wisniewski, Michael
Published in Microorganisms (Basel) (23.06.2020)
Published in Microorganisms (Basel) (23.06.2020)
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Journal Article
High-density NGS-based map construction and genetic dissection of fruit shape and rind netting in Cucumis melo
Oren, Elad, Tzuri, Galil, Dafna, Asaf, Meir, Ayala, Kumar, Ravindra, Katzir, Nurit, Elkind, Yonatan, Freilich, Shiri, Schaffer, Arthur A., Tadmor, Yaakov, Burger, Joseph, Gur, Amit
Published in Theoretical and applied genetics (01.06.2020)
Published in Theoretical and applied genetics (01.06.2020)
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Journal Article
Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation
Ofaim, Shany, Ofek-Lalzar, Maya, Sela, Noa, Jinag, Jiandong, Kashi, Yechezkel, Minz, Dror, Freilich, Shiri
Published in Frontiers in microbiology (23.08.2017)
Published in Frontiers in microbiology (23.08.2017)
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Journal Article
To B or Not to B: Comparative Genomics Suggests Arsenophonus as a Source of B Vitamins in Whiteflies
Santos-Garcia, Diego, Juravel, Ksenia, Freilich, Shiri, Zchori-Fein, Einat, Latorre, Amparo, Moya, Andrés, Morin, Shai, Silva, Francisco J
Published in Frontiers in microbiology (25.09.2018)
Published in Frontiers in microbiology (25.09.2018)
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Journal Article
Modeling trophic dependencies and exchanges among insects' bacterial symbionts in a host-simulated environment
Opatovsky, Itai, Santos-Garcia, Diego, Ruan, Zhepu, Lahav, Tamar, Ofaim, Shany, Mouton, Laurence, Barbe, Valérie, Jiang, Jiandong, Zchori-Fein, Einat, Freilich, Shiri
Published in BMC genomics (25.05.2018)
Published in BMC genomics (25.05.2018)
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Journal Article
Assembly and dynamics of the apple carposphere microbiome during fruit development and storage
Zhimo, V. Yeka, Kumar, Ajay, Biasi, Antonio, Abdelfattah, Ahmed, Sharma, Vijay Kumar, Salim, Shoshana, Feygenberg, Oleg, Bartuv, Rotem, Freilich, Shiri, Whitehead, Susan R., Wisniewski, Michael, Droby, Samir
Published in Frontiers in microbiology (09.08.2022)
Published in Frontiers in microbiology (09.08.2022)
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Journal Article
Variations in the identity and complexity of endosymbiont combinations in whitefly hosts
Zchori-Fein, Einat, Lahav, Tamar, Freilich, Shiri
Published in Frontiers in microbiology (04.07.2014)
Published in Frontiers in microbiology (04.07.2014)
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Journal Article
Transcriptomic Analysis of Soil Grown T. aestivum cv. Root to Reveal the Changes in Expression of Genes in Response to Multiple Nutrients Deficiency
Gupta, Saurabh, Yadav, Brijesh S, Raj, Utkarsh, Freilich, Shiri, Varadwaj, Pritish K
Published in Frontiers in plant science (22.06.2017)
Published in Frontiers in plant science (22.06.2017)
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Journal Article
Construction, visualisation, and clustering of transcription networks from microarray expression data
Freeman, Tom C, Goldovsky, Leon, Brosch, Markus, van Dongen, Stijn, Mazière, Pierre, Grocock, Russell J, Freilich, Shiri, Thornton, Janet, Enright, Anton J
Published in PLoS computational biology (01.10.2007)
Published in PLoS computational biology (01.10.2007)
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Journal Article
A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data
Berihu, Maria, Somera, Tracey S, Malik, Assaf, Medina, Shlomit, Piombo, Edoardo, Tal, Ofir, Cohen, Matan, Ginatt, Alon, Ofek-Lalzar, Maya, Doron-Faigenboim, Adi, Mazzola, Mark, Freilich, Shiri
Published in Microbiome (12.01.2023)
Published in Microbiome (12.01.2023)
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Journal Article
Emergence, development and diversification of the TGF-beta signalling pathway within the animal kingdom
Huminiecki, Lukasz, Goldovsky, Leon, Freilich, Shiri, Moustakas, Aristidis, Ouzounis, Christos, Heldin, Carl-Henrik
Published in BMC evolutionary biology (03.02.2009)
Published in BMC evolutionary biology (03.02.2009)
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Journal Article
Metabolic-network-driven analysis of bacterial ecological strategies
Freilich, Shiri, Kreimer, Anat, Borenstein, Elhanan, Yosef, Nir, Sharan, Roded, Gophna, Uri, Ruppin, Eytan
Published in Genome biology (01.01.2009)
Published in Genome biology (01.01.2009)
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Journal Article