プロフィール詳細

プロジェクトを作成

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Alon P.に依頼

United States

PhD Computational Biologist | Bioinformatics, Machine Learning, AI | Carbon MRV, Scientific & Grant Writing | Python, R

プロフィール概要

PhD scientist offering hands-on data analysis, bioinformatics, machine learning, and scientific and grant writing. I build analytical and machine-learning pipelines in Python and R on HPC clusters. At Caltech and the Technion I assembled and analyzed 4,300+ complete genomes from environmental metagenomes and characterized 160+ novel viral families, working from DNA extraction and next-generation sequencing library preparation (Illumina, Oxford Nanopore) through assembly, annotation, phylogenomics, and statistics. As Founder and CEO of Ecosphere Blue I build EmergentBiome, an inference system on protein and genomic language models (ESM2, gLM2) that predicts methane flux from sediment microbial genomes for blue-carbon MRV under Verra VM0033, and I consult for AI development companies (under NDA) on the accuracy, safety, and security of AI models in biology. I also built climatesolutionsmap.earth, a public interactive map of climate solutions by sector. I write and edit manuscripts, grant proposals, and executive summaries: 15+ peer-reviewed publications including Nature, PNAS, Nature Microbiology, and Current Biology, contributions to multi-million-dollar DOE and NOMIS grants, and reviewer for the NSF, the Czech Science Foundation, Manifest Climate, and 9+ journals. Typical projects: metagenomic, metatranscriptomic, and amplicon (16S) data analysis; genome assembly and annotation; statistical analysis and study design; machine-learning models on biological or environmental data; carbon, GHG, and MRV analysis; literature review and synthesis; manuscript, proposal, and report writing and editing.

専門分野

• ☆ Computational Biology
• ☆ Evolutionary Biology
• ☆ Microbiology
• ☆ Microbiome Research
• ☆ Phycology/Algae
• ☆ Virology
• ☆ Molecular Virology
• ☆ Microbiological Assays
• ☆ Bacteriology
• ☆ Gram-Negative Bacteria
• ☆ Gram-Positive Bacteria
• ☆ Molecular Biology
• ☆ Omics
• ☆ Comparative Genomics
• ☆ PCR
• ☆ Molecular Cloning
• ☆ Next Generation Sequencing (NGS)
• ☆ DNA Sequencing
• ☆ RNA Sequencing
• ☆ Molecular Ecology
• ☆ Marine Biology
• ☆ Microscopy
• ☆ Light Microscopy
• ☆ Electron Microscopy
• ☆ Data Analysis
• ☆ Cluster Analysis
• ☆ Data Visualization
• ☆ Big Data Analytics
• ☆ Data Mining
• ☆ Bioinformatics
• ☆ Systems Biology
• ☆ Earth & Atmospheric Science
• ☆ Biogeochemistry
• ☆ Climate Science
• ☆ Ecology
• ☆ Microbial Ecology
• ☆ Python
• ☆ R
• ☆ Hypothesis
• ☆ Peer Review
• ☆ Research Methodology
• ☆ Meta-Research
• ☆ Technology Scouting
• ☆ Literature Search
• ☆ Scientific Proofreading & Editing
• ☆ Grant Writing

サービス

• Writing
• Research
• Consulting
• Data & AI

Writing Technical Writing

Research Meta-Research, Scientific and Technical Research

Consulting Scientific and Technical Consulting

Data & AI Statistical Analysis, Data Visualization, Data Mining

職務経験

Founder and CEO

Ecosphere Blue

11月 2025 - 現在

Independent Consultant, AI in the Life Sciences

Self employed

9月 2025 - 現在

Postdoc

California Institute of Technology

2月 2018 - 2月 2025

学歴

PhD. (Biology)

Technion Israel Institute of Technology

2009 - 2015

認定資格

• n/a

  n/a

  1月 2026 - 1月 2026

出版物

JOURNAL ARTICLE

Alon Philosof, Maria Alvarez-Sanchez, Francisco Martinez-Hernandez, Aitana Llorenç Vicedo, Marina Vila-Nistal, Aditi K Narayanan, Jamie C Tijerina, Oscar Fornas, Manuel Martinez-Garcia, Victoria J Orphan (2026). Illuminating the newly produced viruses within the virosphere with bioorthogonal noncanonical amino acid tagging and single-virus genomic sequencing technologies . ISME Communications.

Alon Philosof, Aditi K Narayanan, Ranjani Murali, Stephanie A Connon, Gunter Wegener, Victoria J Orphan (2026). Viral communities from long-term anaerobic alkane-oxidizing enrichment cultures encode predicted cell surface adhesion functions . The ISME Journal.

Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes <head> <META HTTP-EQUIV="Refresh" CONTENT="0;URL=/servlet/useragent"> </head> . Nature Microbiology.

Alon Philosof, Gur Hevroni, Jos&#233; Flores-Uribe, Oded B&#233;j&#224; (2020). Seasonal and diel patterns of abundance and activity of viruses in the Red Sea . Proceedings of the National Academy of Sciences.

Hevroni, G., Flores-Uribe, J., B&#233;j&#224;, O., Philosof, A.(2020). Seasonal and diel patterns of abundance and activity of viruses in the Red Sea . Proceedings of the National Academy of Sciences of the United States of America. 117. (47). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 29738-29747.

Flores-Uribe, J., Philosof, A., Sharon, I., Fridman, S., Larom, S., B&#233;j&#224;, O.(2019). A novel uncultured marine cyanophage lineage with lysogenic potential linked to a putative marine Synechococcus ‘relic’ prophage . Environmental Microbiology Reports. 11. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 598-604.

Pushkarev, A., Inoue, K., Larom, S., Flores-Uribe, J., Singh, M., Konno, M., Tomida, S., Ito, S., Nakamura, R., Tsunoda, S.P., et al.(2018). A distinct abundant group of microbial rhodopsins discovered using functional metagenomics . Nature. 558. (7711). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 595-599.

Fridman, S., Flores-Uribe, J., Larom, S., Alalouf, O., Liran, O., Yacoby, I., Salama, F., Bailleul, B., Rappaport, F., Ziv, T., et al.(2017). A myovirus encoding both photosystem i and II proteins enhances cyclic electron flow in infected Prochlorococcus cells . Nature Microbiology. 2. (10). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1350-1357.

Philosof, A., Yutin, N., Flores-Uribe, J., Sharon, I., Koonin, E.V., B&#233;j&#224;, O.(2017). Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota . Current Biology. 27. (9). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1362-1368.

Roitman, S., Flores-Uribe, J., Philosof, A., Knowles, B., Rohwer, F., Ignacio-Espinoza, J.C., Sullivan, M.B., Cornejo-Castillo, F.M., S&#225;nchez, P., Acinas, S.G., et al.(2015). Closing the gaps on the viral photosystem-IpsaDCAB gene organization . Environmental Microbiology. 17. (12). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 5100-5108.

Philosof, A., B&#233;j&#224;, O.(2013). Bacterial, archaeal and viral-like rhodopsins from the Red Sea . Environmental Microbiology Reports. 5. (3). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 475-482.

Feingersch, R., Philosof, A., Mejuch, T., Glaser, F., Alalouf, O., Shoham, Y., B&#233;j&#224;, O.(2012). Potential for phosphite and phosphonate utilization by Prochlorococcus . ISME Journal. 6. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 827-834.

Philosof, A., Battchikova, N., Aro, E.-M., B&#233;j&#224;, O.(2011). Marine cyanophages: Tinkering with the electron transport chain . ISME Journal. 5. (10). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1568-1570.

Man-Aharonovich, D., Philosof, A., Kirkup, B.C., Le Gall, F., Yogev, T., Berman-Frank, I., Polz, M.F., Vaulot, D., B&#233;j&#224;, O.(2010). Diversity of active marine picoeukaryotes in the Eastern Mediterranean Sea unveiled using photosystem-II psbA transcripts . ISME Journal. 4. (8). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1044-1052.

Philosof, A., Sabehi, G., B&#233;j&#224;, O.(2009). Comparative analyses of actinobacterial genomic fragments from Lake Kinneret . Environmental Microbiology. 11. (12). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 3189-3200.

PREPRINT

Alon Philosof, Maria Alvarez-Sanchez, Francisco Martinez-Hernandez, Aitana Lloren&#231; Vicedo, Marina Vila-Nistal, Aditi K. Narayanan, Jamie C. Tijerina, Manuel Martinez-Garcia, Victoria J Orphan (2025). Illuminating the active virosphere with BONCAT and single virus genomic sequencing technologies .

Alon Philosof, Aditi K. Narayanan, Ranjani Murali, Stephanie A. Connon, Gunter Wegener, Victoria J. Orphan (2025). Viral communities from long-term anaerobic alkane-oxidizing enrichments may promote cell surface adhesion .

OTHER

Alon Philosof, Gur Hevroni, Jos&#233; Flores-Uribe, Oded B&#233;j&#224;(2020). Rising through the Ranks: Seasonal and Diel Patterns of Marine Viruses . Cold Spring Harbor Laboratory