Recent Publications


The most updated list of publications by the Northen Lab is available via google scholar.

2017

Heinemann, J., Deng, K., Shih, S. C. C., Gao, J., Adams, P. D., Singh, A. K., and Northen, T. R. (2017) On-chip integration of droplet microfluidics and nanostructure-initiator mass spectrometry for enzyme screening. Lab Chip 17, 323–331. DOI: 10.1039/C6LC01182A

Yuzawa, S., Deng, K., Wang, G., Baidoo, E. E. K., Northen, T. R., Adams, P. D., Katz, L., and Keasling, J. D. (2017) Comprehensive in Vitro Analysis of Acyltransferase Domain Exchanges in Modular Polyketide Synthases and Its Application for Short-Chain Ketone Production. ACS Synth. Biol. 6, 139–147. DOI: 10.1021/acssynbio.6b00176.

Walker, J. A., Pattathil, S., Bergeman, L. F., Beebe, E. T., Deng, K., Mirzai, M., Northen, T. R., Hahn, M. G., and Fox, B. G. (2017) Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling. Biotechnol. Biofuels 10. DOI: 10.1186/s13068-017-0703-6

 

2016

Hiras, J., Wu, Y. W., Deng, K., Nicora, C. D., Aldrich, J. T., Frey, D., Kolinko, S., Robinson, E. W., Jacobs, J. M., Adams, P. D., Northen, T. R., Simmons, B. A., and Singer, S. W. (2016) Comparative community proteomics demonstrates the unexpected importance of actinobacterial glycoside hydrolase family 12 protein for crystalline cellulose hydrolysis. MBio 7, 1–9. DOI: 10.1128/mBio.01106-16

 

Kosina, S. M., Danielewicz, M. A., Mohammed, M., Ray, J., Suh, Y., Yilmaz, S., Singh, A. K., Arkin, A. P., Deutschbauer, A. M., and Northen, T. R. (2016) Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism. ACS Synth. Biol. 5, 569–576. DOI: 10.1021/acssynbio.5b00236

Lubbe, A., and Northen, T. (2016) Exometabolomics for Linking Soil Carbon to Microbial Communities, in Microbial Metabolomics (Al., D. J. B. et, Ed.), pp 119–145. Springer International Publishing.

Gao J, de Raad M, Bowen BP, Zuckermann RN, Northen TR. Application of black silicon for nanostructure-initiator mass spectrometry. Analytical Chemistry, 2016 88(3) 1625-1630 DOI: 10.1021/acs.analchem.5b03452

Walker JA, Takasuka TE, Deng K, Bianchetti CM, Udell HS, Prom BM, Kim H, Adams PD, Northen TR, Fox BG. Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules. Biotechnol Biofuels. 2015 Dec 21;8:220. DOI: 10.1186/s13068-015-0402-0

Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams PD, Northen TR, Fox BG. Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases. Front Bioeng Biotechnol. 2015 Oct 27;3:165. DOI: 10.3389/fbioe.2015.00165

de Raad M, Fischer CR, Northen TR. High-throughput platforms for metabolomics. Curr Opin Chem Biol. 2016 Feb;30:7-13. DOI: 10.1016/j.cbpa.2015.10.012

Deng K, Guenther JM, Gao J, Bowen BP, Tran H, Reyes-Ortiz V, Cheng X, Sathitsuksanoh N, Heins R, Takasuka TE, Bergeman LF, Geertz-Hansen H, Deutsch S, Loqué D, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR. Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS. Front Bioeng Biotechnol. 2015 Oct 13;3:153. doi: 10.3389/fbioe.2015.00153

2015

Baran R, Brodie EL, Mayberry-Lewis J, Hummel E, Nunes Da Rocha U, Chakraborty R, Bowen BP, Karaoz U, Cadillo-Quiroz H, Garcia-Pichel F, Northen TR. Exometabolite niche partitioning among sympatric soil bacteria. Nature Communications, 2015 6(6):8289 DOI:10.1038/ncomms9289

Ceja-Navarro, J. A., F. E. Vega, U. Karaoz, Z. Hao, S. Jenkins, H. C. Lim, P. Kosina, F. Infante, T. R. Northen, and E. L. Brodie. Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee. Nature Communications, 2015, 6:7618. doi:10.1038/ncomms8618

Yee Ngan CY, Wong CH, Choi C, Yoshinaga Y, Louie K, Jia J, Chen C, Bowen B, Cheng H, Leonelli L, Kuo R, Baran R, JGarcía-Cerdán J,Pratap A, Mei Wang1, Joanne Lim1, Hope Tice1, Daum C, Xu J, Northen TR, Visel A, Bristow J, Niyogi K, Wei CL. Lineage-Specific Chromatin Signatures Reveal a Regulator of Lipid Metabolism in Microalgae. Nature Plants 2015, 1:15107, doi:10.1038/nplants.2015.107

Ulisses Nunes da Rocha, Hinsby Cadillo-Quiroz, Ulas Karaoz, Lara Rajeev, Niels Klitgord, Sean Dunn, Viet Truong, Mayra Buenrostro, Benjamin Paul Bowen, Ferran Garcia-Pichel, Aindrila Mukhopadhyay, Trent Russell Northen*, Eoin L Brodie*. Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust. Frontiers in Microbiology. 2015 http://dx.doi.org/10.3389/fmicb.2015.00277

Silva L, Northen TR. Exometabolomics and MSI: deconstructing how cells interact to transform their small molecule environment. Current Opinion in Biotechnology. 2015 34, 209-216 doi:10.1016/j.copbio.2015.03.015

Bowen B*, Yao Y, Sun T, Wang T, Ruebel O, Northen T. Analysis of metabolomics datasets with high-performance computing and Metabolite Atlases. Metabolites, 2015, Metabolites 5 (3) 431-442. doi:10.3390/metabo5030431

Swenson, T. L., Jenkins, S., Bowen, B. P., and Northen, T. R. (2015) Untargeted soil metabolomics methods for analysis of extractable organic matter. Soil Biol. Biochem. 80, 189–198. DOI: 10.1016/j.soilbio.2014.10.007

Swenson, T. L., Bowen, B. P., Nico, P. S., and Northen, T. R. (2015) Competitive sorption of microbial metabolites on an iron oxide mineral. Soil Biol. Biochem. 90, 34–41. doi:10.1016/j.soilbio.2015.07.022

Kurczy M., Northen T., Trauger, S.A., Siuzdak, G. Nanostructure Imaging Mass Spectrometry: The Role of Fluorocarbons in Metabolite Analysis and the Road to Yoctomole Level Sensitivity. Methods in Mol. Bio. , 2015 1203, 141-149. doi: 10.1007/978-1-4939-1357-2_14.

Castellanos-Martín, Castillo-Lluva, del Mar Sáez-Freire, Blanco-Gómez, Hontecillas-Prieto, Patino-Alonso, Galindo-Villardon, Pérez del Villar, Carmen Martín-Seisdedos2,6, María Isidoro-Garcia, del Mar Abad-Hernández, Cruz-Hernández, Rodríguez-Sánchez, González-Sarmiento, Alonso-López, De Las Rivas, García-Cenador, Lee, Bowen, Reindl, Northen*, Mao*, Pérez-Losada* Unraveling heterogeneous susceptibility and the evolution of breast cancer by a systems biology approach. Genome Biology 2015 16, 40 2-23 doi:10.1186/s13059-015-0599-z

Sylvie Miquel, Marion Leclerc, rebeca Martin, Florian Chain, Marion Lenoir, Sébastien Raguideau, Sylvie Hudault, Chantal Bridonneau, Trent Northen, Benjamin Bowen, Luis G. Bermúdez-Humarán, Harry Sokol, Muriel Thomas, and Philippe Langella. Identification of metabolic signatures linked to anti-inflammatory effects of Faecalibacterium prausnitzii mBio 2015, 6 (2) doi: 10.1128/mBio.00300-15

De Rond T, Danielwicz M, Northen T. High throughput screening of enzyme activity with mass spectrometry imaging. Current Opinion in Biotechnology. Current opinion in biotechnology 2015 31, 1-9. DOI: 10.1016/j.copbio.2014.07.008

2014

Deng K, Takasuka TE, Heins R, Cheng X, Bergeman LF, Shi J, Aschenbrener R, Deutsch S, Singh S, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR. Rapid Kinetic Characterization of Glycosyl hydrolases (GHs) based on Oxime Derivatization and Nanostructure-Initiator Mass Spectrometry (NIMS). ACS Chemical Biology 2014, 9(7), 1470-1479 DOI: 10.1021/cb5000289 (Cover)

Heins R, Cheng X, Nath S, Deng K, Bowen B; Chivian D, Datta S, Friedland G, D’Haeseleer P, Wu D, Tran-Gyamfi M, Scullin C, Singh S, Shi W, Hamilton M, Bendall M, Sczyrba A, Thompson J, Feldman T, Guenther J, Gladden J, Cheng JF, Adams P, Rubin E, Simmons BA, Sale K, Northen, T, Deutsch S. Phylogenomic Guided Identification of Industrially Relevant GH1 β-Glucosidases Through Coupled DNA Synthesis and Nanostructure-Initiator Mass Spectrometry. ACS Chemical Biology 2014, 19(9), 2082-91. DOI: 10.1021/cb500244v

Vandehey, Nicholas; Brodie, Eoin; Northen, Trent; O’Neil, James. Non-invasive Mapping of Photosynthetic Heterogeneity in Biological Soil Crusts by Positron Emission Tomography: Carbon Fixation. Environmental Science & Technology Letters, 2014, 1(10) 393-398. DOI: 10.1021/ez500209c

Berleman J, Allen S, Danielewicz M, Remis J, Gorur A, Cunha J, Hadi M, Zusman D, Northen T, Witkowska H. Ewa, Manfred Auer, The Lethal Cargo of Myxococcus xanthus Outer Membrane Vesicles, Frontiers in Microbiology 2014, 5, 274, 1-11. doi: 10.3389/fmicb.2014.00474

2013

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.

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

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

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

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.

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

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.

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

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

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

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

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

2012

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, 4765-4779 DOI:10.1038/onc.2011.196

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 Spectrometry2012 Mar 30;26(6):611-5. DOI: 10.1002/rcm.6134.

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

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

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

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

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

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.

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