Oslo, Norway
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Nolan Newman, Ph.D.
Computational Biologist | Breast Cancer and Network Biology
Causal inference
Network biology
Data mining
Pipeline development
Python and R
16S gut microbiome analysis
About me
I am a postdoctoral researcher at the University of Oslo, studying tumor heterogeneity in breast cancer through the reconstruction and comparison of single sample regulatory networks. My work has included the development of the SiSaNA pipeline, which is software that helps users reconstruct single sample regulatory networks all via a command line interface, without the need of prior programming experience. During my PhD, I developed software for reconstructing gene-microbe co-variation networks, utilizing system biology and network biology to identify genes and microbes driving disease and treatment response. I am particularly interested in building robust, reproducible pipelines that reveal novel therapeutic targets in cancer and metabolic disease.
Education
Ph.D., Pharmaceutical Sciences - Computational Biology
Sept. 2023
Oregon State University, Corvallis, OR, USA
Dissertation: Development and implementation of a transkingdom network analysis pipeline to identify drivers of disease.
Advisor: Dr. Andrey Morgun
M.S., Pharmaceutical Sciences - Computational Biology
June 2021
Oregon State University, Corvallis, OR, USA
B.S., Biology - Pre-Medicine
June 2018
Eastern Washington University, Cheney, WA, USA
Experience
Postdoctoral researcher
2023-Present
Norwegian Centre for Molecular Biosciences and Medicine (University of Oslo)
Oslo, Norway
- Reconstructed and analyzed gene regulatory networks from single individuals to help identify additional subtypes of breast cancer patients
- Developed the SiSaNA (Single-Sample Network Analysis) pipeline to help streamline the process of reconstructing single-sample regulatory networks
PhD candidate in Pharmaceutical Sciences
2018-2023
Oregon State University
Corvallis, OR, USA
- Reconstructed transkingdom networks to identify genes and microbes essential for the development of diseases and/or the response to medication
- Developed the TkNA (Transkingdom Network Analysis) pipeline (https://github.com/CAnBioNet/TkNA)
Graduate Teaching Assistant - Terminology of the Health Sciences
2019-2023
Oregon State University
Corvallis, OR, USA
- Lectured the course, designed slides/study material, and wrote/graded exams
Skills
Programming & Computing:
- Proficient in Python, R, and Bash
- Knowledge of critical programming methodologies such as TDD and CI/CD
- GitHub, Docker, and Jira
- HPC/cluster environments
Data Science & Analytics:
- Causal inference
- Machine learning
- Data mining on publicly available datasets
- Development and maintenance of reproducible analysis pipelines
Bioinformatics:
- Transcriptomic analysis (QC, read mapping/assembly, expression quantification, downstream analysis)
- 16S gut microbiome analysis (QC, taxonomic profiling, downstream statistical analysis)
- scRNA-Seq analysis
- Biological network reconstruction and interrogation
Project management:
- Coordinating research projects and papers, defining deadlines and deliverables
- Organizing meetings
- Collaborating via Trello/Jira boards
- Translating and reporting key research findings for others
Selected publications
General publication info: (9) Research Articles |
🖉 (5) First Author |
(1) Preprint
🖉
SiSaNA: A Python-based command line interface for Single-Sample Network Analysis
2026
DOI:
10.1101/2025.11.06.680212
Authors: Newman, N.K., Belova, T., Kuijjer, M.L.
🖉
Transkingdom Network Analysis (TkNA): A systems framework for inferring causal factors underlying host–microbiota and other multi-omic interactions
2024
DOI:
10.1038/s41596-024-00960-w
Authors: Newman, N.K., Macovsky, M.S., Rodrigues, R.R., Bruce, A.M., Pederson, J.W., Padiadpu, J., Shan, J., Williams, J., Patil, S.S., Dzutsev, A.K., Shulzhenko, N., Brown. K., Morgun, A.
Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1
2022
DOI:
10.1038/s41591-022-01698-2
Authors: McCulloch, J.A., Davar, D., Rodrigues, R.R., Badger, J.H., Fang, J.R., Cole, A.M., Balaji, A.K., Vetizou, M., Prescott, S.M., Fernandes, M.R., Costa, R.G.F., Yuan, W., Salcedo, R., Bahadiroglu, E., Roy, S., DeBlasio, R.N., Morrison, R.M., Chauvin, J.-M., Ding, Q., Zidi, B., Lowin, A., Chakka, S., Gao, W., Pagliano, O., Ernst, S.J., Rose, A., Newman, N.K., Morgun, A., Zarour, H.M., Trinchieri, G., Dzutsev, A.K.
Causal inference
Network biology
Data mining
Pipeline development
Python and R
16S gut microbiome analysis
About me
I am a postdoctoral researcher at the University of Oslo, studying tumor heterogeneity in breast cancer through the reconstruction and comparison of single sample regulatory networks. My work has included the development of the SiSaNA pipeline, which is software that helps users reconstruct single sample regulatory networks all via a command line interface, without the need of prior programming experience. During my PhD, I developed software for reconstructing gene-microbe co-variation networks, utilizing system biology and network biology to identify genes and microbes driving disease and treatment response. I am particularly interested in building robust, reproducible pipelines that reveal novel therapeutic targets in cancer and metabolic disease.
Education
Ph.D., Pharmaceutical Sciences - Computational Biology
Oregon State University, Corvallis, OR, USA Sept. 2023
Dissertation: Development and implementation of a transkingdom network analysis pipeline to identify drivers of disease.
Advisor: Dr. Andrey Morgun
M.S., Pharmaceutical Sciences - Computational Biology
Oregon State University, Corvallis, OR, USA
June 2021
B.S., Biology - Pre-Medicine
Eastern Washington University, Cheney, WA, USAJune 2018
Experience
Postdoctoral researcher
Norwegian Centre for Molecular Biosciences and Medicine (University of Oslo)
2023-Present
Oslo, Norway
- Reconstructed and analyzed gene regulatory networks from single individuals to help identify additional subtypes of breast cancer patients
- Developed the SiSaNA (Single-Sample Network Analysis) pipeline to help streamline the process of reconstructing single-sample regulatory networks
PhD candidate in Pharmaceutical Sciences
Oregon State University2018-2023
Corvallis, OR, USA
- Reconstructed transkingdom networks to identify genes and microbes essential for the development of diseases and/or the response to medication
- Developed the TkNA (Transkingdom Network Analysis) pipeline (https://github.com/CAnBioNet/TkNA)
Graduate Teaching Assistant - Terminology of the Health Sciences
Oregon State University2019-2023
Corvallis, OR, USA
- Lectured the course, designed slides/study material, and wrote/graded exams
Skills
Programming & Computing:
- Proficient in Python, R, and Bash
- Knowledge of critical programming methodologies such as TDD and CI/CD
- GitHub, Docker, and Jira
- HPC/cluster environments
Data Science & Analytics:
- Causal inference
- Machine learning
- Data mining on publicly available datasets
- Development and maintenance of reproducible analysis pipelines
Bioinformatics:
- Transcriptomic analysis (QC, read mapping/assembly, expression quantification, downstream analysis)
- 16S gut microbiome analysis (QC, taxonomic profiling, downstream statistical analysis)
- scRNA-Seq analysis
- Biological network reconstruction and interrogation
Project management:
- Coordinating research projects and papers, defining deadlines and deliverables
- Organizing meetings
- Collaborating via Trello/Jira boards
- Translating and reporting key research findings for others
Selected publications
General publication info: (9) Research Articles |
🖉 (5) First Author |
(1) Preprint
🖉
SiSaNA: A Python-based command line interface for Single-Sample Network Analysis
DOI:
10.1101/2025.11.06.680212
2026
Authors: Newman, N.K., Belova, T., Kuijjer, M.L.
🖉
Transkingdom Network Analysis (TkNA): A systems framework for inferring causal factors underlying host–microbiota and other multi-omic interactions
DOI:
10.1038/s41596-024-00960-w
2024
Authors: Newman, N.K., Macovsky, M.S., Rodrigues, R.R., Bruce, A.M., Pederson, J.W., Padiadpu, J., Shan, J., Williams, J., Patil, S.S., Dzutsev, A.K., Shulzhenko, N., Brown. K., Morgun, A.
Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1
DOI:
10.1038/s41591-022-01698-2
2022
Authors: McCulloch, J.A., Davar, D., Rodrigues, R.R., Badger, J.H., Fang, J.R., Cole, A.M., Balaji, A.K., Vetizou, M., Prescott, S.M., Fernandes, M.R., Costa, R.G.F., Yuan, W., Salcedo, R., Bahadiroglu, E., Roy, S., DeBlasio, R.N., Morrison, R.M., Chauvin, J.-M., Ding, Q., Zidi, B., Lowin, A., Chakka, S., Gao, W., Pagliano, O., Ernst, S.J., Rose, A., Newman, N.K., Morgun, A., Zarour, H.M., Trinchieri, G., Dzutsev, A.K.