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 applied systems and network biology to gut microbiome and host multi-omics data 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
Publications
(9) Research Articles |
🖉 (5) First Author |
(1) Preprint
🖉
SiSaNA: A Python-based command line interface for Single-Sample Network Analysis
2025
DOI:
10.1101/2025.11.06.680212
Authors: Newman, N.K., Belova, T., Kuijjer, M.L.
🖉
Host response to cholestyramine can be mediated by the gut microbiota
2024
DOI:
10.20517/mrr.2023.82
Authors: Newman, N.K., Monnier, P.M., Rodrigues, R.R., Gurung, M., Vasquez-Perez, S., Hioki, K.A., Greer, R.L., Brown. K., Morgun, A., and Shulzhenko, N.
🖉
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.
Multi‐omic network analysis identified betacellulin as a novel target of omega‐3 fatty acid attenuation of western diet‐induced nonalcoholic steatohepatitis
2023
DOI:
10.15252/emmm.202318367
Authors: Padiadpu, J., Garcia‐Jaramillo, M., Newman, N.K., , Pederson, J.W., Rodrigues, R., Li, Z., Singh, S., Monnier, P., Trinchieri, G., Brown, K., Dzutsev, A.K., Shulzhenko, N., Jump, D.B., Morgun, A.
🖉
Reducing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome
2023
DOI:
10.1186/s40168-023-01637-4
Authors: Newman, N.K., Zhang, Y., Padiadpu, J., Miranda, C.L., Magana, A.A., Wong, C.P., Hioki, K.A., Pederson, J.W., Li, Z., Gurung, M., Bruce, A.M., Brown, K., Bobe, G., Sharpton, T.J., Shulzhenko, N., Maier, C.S., Stevens, J.F., Gombart, A.F., Morgun, A.
Early transcriptome changes associated with western diet induced NASH in Ldlr−/− mice points to activation of hepatic macrophages and an acute phase response
2023
DOI:
10.3389/fnut.2023.1147602
Authors: Padiadpu, J., Spooner, M.H., Li, Z., Newman, N.K., Löhr, C.V., Apperson, K.D., Dzutsev, A., Trinchieri, G., Shulzhenko, N., Morgun, A., Jump, D.B.
Microbiota and adipocyte mitochondrial damage in type 2 diabetes are linked by Mmp12+ macrophages
2022
DOI:
10.1084/jem.20220017
Authors: Li, Z., Gurung, M., Rodrigues, R.R., Padiadpu, J., Newman, N.K., Manes, N.P., Pederson, J.W., Greer, R.L., Vasquez-Perez, S., You, H., Hioki, K.A., Moulton, Z., Fel, A., De Nardo, D., Dzutsev, A.K., Nita-Lazar, A., Trinchieri, G., Shulzhenko, N., 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.
🖉
Dietary indole-3-carbinol activates AhR in the gut, alters Th17-microbe interactions, and exacerbates insulitis in NOD mice
2021
DOI:
10.3389/fimmu.2020.606441
Authors: Kahalehili, H.M., Newman, N.K., Pennington, J.M., Kolluri, S.K., Kerkvliet, N.I., Shulzhenko, N., Morgun, A., and Ehrlich, 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 applied systems and network biology to gut microbiome and host multi-omics data 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
Publications
(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
2025
Authors: Newman, N.K., Belova, T., Kuijjer, M.L.
🖉
Host response to cholestyramine can be mediated by the gut microbiota
DOI:
10.20517/mrr.2023.82
2024
Authors: Newman, N.K., Monnier, P.M., Rodrigues, R.R., Gurung, M., Vasquez-Perez, S., Hioki, K.A., Greer, R.L., Brown. K., Morgun, A., and Shulzhenko, N.
🖉
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.
Multi‐omic network analysis identified betacellulin as a novel target of omega‐3 fatty acid attenuation of western diet‐induced nonalcoholic steatohepatitis
DOI:
10.15252/emmm.202318367
2023
Authors: Padiadpu, J., Garcia‐Jaramillo, M., Newman, N.K., , Pederson, J.W., Rodrigues, R., Li, Z., Singh, S., Monnier, P., Trinchieri, G., Brown, K., Dzutsev, A.K., Shulzhenko, N., Jump, D.B., Morgun, A.
🖉
Reducing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome
DOI:
10.1186/s40168-023-01637-4
2023
Authors: Newman, N.K., Zhang, Y., Padiadpu, J., Miranda, C.L., Magana, A.A., Wong, C.P., Hioki, K.A., Pederson, J.W., Li, Z., Gurung, M., Bruce, A.M., Brown, K., Bobe, G., Sharpton, T.J., Shulzhenko, N., Maier, C.S., Stevens, J.F., Gombart, A.F., Morgun, A.
Early transcriptome changes associated with western diet induced NASH in Ldlr−/− mice points to activation of hepatic macrophages and an acute phase response
DOI:
10.3389/fnut.2023.1147602
2023
Authors: Padiadpu, J., Spooner, M.H., Li, Z., Newman, N.K., Löhr, C.V., Apperson, K.D., Dzutsev, A., Trinchieri, G., Shulzhenko, N., Morgun, A., Jump, D.B.
Microbiota and adipocyte mitochondrial damage in type 2 diabetes are linked by Mmp12+ macrophages
DOI:
10.1084/jem.20220017
2022
Authors: Li, Z., Gurung, M., Rodrigues, R.R., Padiadpu, J., Newman, N.K., Manes, N.P., Pederson, J.W., Greer, R.L., Vasquez-Perez, S., You, H., Hioki, K.A., Moulton, Z., Fel, A., De Nardo, D., Dzutsev, A.K., Nita-Lazar, A., Trinchieri, G., Shulzhenko, N., 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.
🖉
Dietary indole-3-carbinol activates AhR in the gut, alters Th17-microbe interactions, and exacerbates insulitis in NOD mice
DOI:
10.3389/fimmu.2020.606441
2021
Authors: Kahalehili, H.M., Newman, N.K., Pennington, J.M., Kolluri, S.K., Kerkvliet, N.I., Shulzhenko, N., Morgun, A., and Ehrlich, A.K.