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Northen Lab

Research Interest

We are interested in metabolic state changes as cells respond perturbations in nutrient availability to environmental stresses and how cooperation improves metabolic efficiency and robustness. Central to these efforts are the development of experimental and computational approaches to study these processes using mass spectrometry based metabolite and activity profiling, stable isotope tracing, and mass spectrometry imaging. Together these allow us to comprehensively characterize metabolic activities, dynamics and localization within complex cellular systems to predict responses and design interventions.

Microbial Community


Recent Publications

2011 - present:

Cheng X, Hiras J, Deng K, Simmons BA,Adams PD, Singer SW and Northen TR. HT NIMS screening of environmental microbial isolate growth conditions for maximal enzyme activity. Frontiers in Microbiology (Accepted)    

Oliver Rübel, Annette Greiner, Shreyas Cholia, Katherine Louie, E. Wes Bethel, Trent R. Northen, and Benjamin P. Bowen, OpenMSI: High-performance web-based visualization, analysis and management of mass spectrometry imaging data, Analytical Chemistry, 2013 85(21):10354-61. doi: 10.1021/ac402540a.

Katherine B. Louie, Benjamin P. Bowen, Xiaoliang Cheng, James Berleman, Romy Chakraborty, Adam Deutschbauer, Adam Arkin and Trent R. Northen. Replica-extraction-transfer’ for nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria and microbial communities, Analytical Chemistry  2013, 85(22) 10856-62. DOI: 10.1021/ac402240q

Baran R, Ivanova N, Jose N, Garcia-Pichel F, Kyrpides N, Gugger M, Northen T. Functional genomics of novel secondary metabolites from diverse cyanobacteria using untargeted metabolomics. Marine Drugs 2013, 11(10), 3617-3631; doi:10.3390/md11103617

Baran, R, Northen, T. Robust Automated Mass Spectra Interpretation and Chemical Formula Calculation Using Mixed Integer Linear Programming. Analytical Chemistry 2013, 85 (20), pp 9777–9784 DOI: 10.1021/ac402180c

Fischer CR, Bowen BP, Pan C, Northen TR, Banfield JF Stable-isotope probing reveals hydrogen isotope fractionation in proteins and lipids in a microbial community are different and species-specific, ACS Chemical Biology 2013, 8 (8), 1755–1763 DOI: 10.1021/cb400210q

Rajeev L, Nunes da Rocha U, Klitgord N, Luning EG, Fortney J, Axen SP, Shih PM, Bouskill NJ, Bowen BP, Kerfield C, Ferran Garcia-Pichel F, Brodie EL,  Northen TR, Mukhopadhyay, A. Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust, ISME Journal, 2013  7, 2178–2191; doi:10.1038/ismej.2013.83

Ho JC, Storm P, Rydström A, Bowen B, Alsin F, Sullivan L, Ambite I, Mok KH, Northen T, Svanborg C. Lipids as tumoricidal components of human alpha-lactalbumin made leathal to tumor cells (HAMLET): unique and shared effects on signaling and death. J Biol Chem. 2013 Jun 14;288(24):17460-71. doi: 10.1074/jbc.M113.468405. Epub 2013 Apr 29.

Louie KB, Bowen BP, McAlhany S,  Huang Y, Mao JH, Hellerstein M and Northen TR  Kinetic mass spectrometry imaging for in situ kinetic histochemistry, Nature Scientific Reports, 2013 Apr 15;3:1656  PMCID: PMC3625901  DOI: 10.1038/srep01656

Ryan P. McAndrew, Joshua Park, Wolfgang Reindl, Gregory D. Friedland, Patrik D’haeseleer, Trent Northen, Kenneth L. Sale, Blake A. Simmons, and Paul D. Adams. From soil to structure: a novel dimeric family 3 β-glucosidase isolated from compost using metagenomics. Journal of Biochemistry, 2013,288(21):14985-92. doi: 10.1074/jbc.M113.458356.

De Rond T, Peralta-Yahya P, Cheng X, Northen TR, Keasling JD. Versatile synthesis of probes for high-throughput enzyme activity screening. Anal Bioanl Chemistry, 2013 May;405(14):4969-73. DOI: 10.1007/s00216-013-6888-z

Mosier AC, Justice NB, Bowen BP, Baran R, Thomas BC, Northen TR, Banfield JF. Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable isotope enabled metabolomics. 2013 Mar 12;4(2):e00484-12 PMCID: PMC3604775  DOI: 10.1128/mBio.00484-12

Baran R, Bowen BP, Price MN, Arkin AP, Deutschbauer AM, Northen TR.   Metabolic Footprinting of Mutant Libraries To Map Metabolite Utilization to Genotype. ACS Chemical Biology.  2013, 8 (1), 189-199.  DOI: 10.1021/cb300477w

Kamennaya N, Ajo-franklin C, Northen T, Jansson C.  Biomineralization by Calcifying Cyanobacteria - a Potential Means for Biological Carbon Capture and Storage. Minerals. 2012, 2(4), 338-364; doi:10.3390/min2040338

Lee DY, Bowen B, Louie K, Nguyen, D, Parsa S, Huang Y, Mao JH, Northen T. Low-dose ionizing radiation-induced blood plasma metabolic response in a diverse genetic mouse population. Radiation Research, 2012 Dec;178(6):551-5. DOI: 10.1667/RR2990.1.

Lee DY, Platt V, Bowen B, Louie K, Canaria C, McMurray C, Northen T. Resolving brain regions using nanostructure initiator mass spectrometry imaging of phospholipids. Integrative Biology 2012, 4 (6), 693 – 699  DOI: 10.1039/c2ib20043k

Reindl W, Deng K, Cheng X, Singh AK, Simmons B, Adams P, Northen T Nanostructure-Initiator Mass Spectrometry (NIMS) for the Analysis of Enzyme Activities, Curr. Protocols in Chem. Biology, 2012, 4:123‐142 DOI: 10.1002/9780470559277.ch110221

Greving M, Cheng K, Reindl W, Bowen B, Deng D, Louie K, Nyman M, Cohen J, Singh A, Simmons B, Adams P, Siuzdak G, and Northen T Acoustic deposition with NIMS as a high throughput enzyme activity assay, Anal Bioanl Chemistry 2012 May;403(3):707-11. Epub 2012 Mar 10.  DOI: 10.1007/s00216-012-5908-8

Patti G.J, Tautenhahn R., Fonslow B.R., Cho Y., Deutschbauer A., Arkin A., Northen T., Siuzdak G. Meta-Analysis of Global Metabolomics and Proteomics Data to Link Alterations with Phenotype Spectroscopy (cover article), 2011, 26(3), 151-154      

Fischer CR, Wilmes P, Bowen BP, Northen TR, Banfield JF. Deuterium Exchange Metabolomics Identifies N-Methyl lyso Phosphatidylethanolamines As Abundant Lipids in Acidophilic Mixed Microbial Communities. 2012 8 (4) 566-578. DOI: 10.1007/s11306-011-0344-x

Deng K, George KW, Reindl W, Keasling JD,  Adams PA, Lee TS, Singh AK, Northen TR, Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme, Rapid Comm. Mass Spectrometry 2012 Mar 30;26(6):611-5. DOI: 10.1002/rcm.6134.

Storm, P; Aits, S; Puthia, MK; Urbano, A; Northen, T; Powers, S; Bowen, B; Chao, Y;  Reindl, W; Lee, DY; Sullivan, NL; Zhang, L; Trulsson, M; Yang, H; Watson, JD; and  Svanborg; C. Conserved features of cancer cells define their sensitivity to HAMLET-induced death; c-Myc and glycolysis. Oncogene 30. (2011). 4765-4779 DOI:10.1038/onc.2011.196

Baran, Richard, Bowen, Benjamin, Northen, Trent R. Untargeted metabolic footprinting reveals a surprising breadth of metabolite uptake and release by Synechococcus sp. PCC 7002. Molecular BioSystems 2011,7, 3200-3206 DOI: 10.1039/c1mb05196b

Wolfgang Reindl, Kai Deng, John M. Gladden, Gang Cheng, April Wong, Steven W. Singer, Seema Singh, Jinq-Chyi Lee, Chun-Hsu Yao, Terry C. Hazen, Anup K. Singh, Blake A. Simmons, Paul D. Adams and Trent R. Northen. Colloid-based multiplexed screening for plant biomass-degrading glycoside hydrolase activities in microbial communities. Energy and Envir.Sci. (2011), 4, 2884-2893.  DOI: 10.1039/C1EE01112J

Bowen, B., Fischer, C., Baran, R., Banfield, J., & Northen, T. (2011). Improved genome annotation through untargeted detection of pathway-specific metabolites. BMC Genomics, 12(Suppl 1), S6. BioMed Central Ltd. doi:10.1186/1471-2164-12-S1-S6  PMCID: PMC32223729  DOI: 10.1186/1471-2164-12-S1-S6

Reindl, Wolfgang E; Bowen, Benjamin, P; Balamontis, Michael A; Green, Jeffery, E; Northen, Trent R. Multivariate analysis of a 3D mass spectral image for examining tissue heterogeneity. Integrative Biology (2011). 3: 460-467.  PMCID: PMC3495549 DOI: 10.1039/c0ib00091d


Updated March 14, 2014


Trent Northen

Staff Scientist/
Life Sciences Division

Genome Dynamics

Berkeley Lab
One Cyclotron Road
Mailstop: 977
Berkeley, CA 94720
Tel: (510) 486-5240/6048
Fax: (510) 486-4545
Website Northen lab:
Website mass spectrometry:


Lab Members

Principal Scientist
Northen, Trent

Research Scientist
Bowen, Ben

Project Scientist
Jenkins, Stefan

Postdoctoral Fellows
Baran, Richard
Cheng, Xiaoliang
Danielewicz, Megan
Louie, Katherine
Mohammed, Mujahid
Rademacher, Pete
Swenson, Tami

Project Manager
Tanamachi, Jane