Graduate Student
I am graduate student in Bioengineering. My research interests include integrating high throughput data with in silico models of metabolism and transcriptional regulation for probing into neurodegenerative disease, studying laboratory evolution, and protein glycoslyation. In my free time I love cracking open science textbooks for leisure reading, hiking and biking, snorkeling in the La Jolla cove, and just spending time with my wife Maria and our daughters Anabelle and Livya.
Education
2006-present Ph.D. Bioengingeering spec. Bioinformatics, Univ of California, San Diego, GPA: 3.81
2008 M.S. Bioengingeering, Univ of California, San Diego, GPA: 3.81
1998-2006 B.S. Biochemistry, cum laude, Brigham Young University, GPA: 3.85
Publications
Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols, (2011).
Xu X*, Nagarajan H*, Lewis NE *, Pan S*, Cai Z*, Liu X, Chen W, Xie M, Wang W, Hammond S, Andersen MR, Neff N, Passarelli B, Koh W, Fan HC, Wang J, Gui Y, Lee KH, Betenbaugh MJ, Quake SR, Famili I, Palsson BO, Wang J. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nature Biotechnology, (2011). * equal contribution
Conrad TM, Lewis NE, Palsson BØ. Microbial laboratory evolution in the era of genome-scale science. Molecular Systems Biology, (2011).
Nam H*, Conrad TM, Lewis NE*#. The role of cellular objectives and selective pressures in metabolic pathway evolution. Current Opinions in Biotechnology, (2011). * equal contribution, # corresponding author
Schellenberger J, Lewis NE, Palsson BØ. Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophysical Journal, 100(3):544-53 (2011).
Lewis NE, Schramm G, Bordbar A, Schellenberger J, Andersen MP, Cheng JK, Patel N, Yee A, Lewis RA, Eils R, König R, Palsson BO. Large-scale in silico modeling of metabolic interactions between cell types in the human brain, Nature Biotechnology, 28 (12):1279–1285 (2010). **Research highlighted by UCSD Jacobs School of Engineering and Nature Methods.
Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol Syst Bio, 6:422 (2010).
Conrad TM, Frazier M, Joyce A, Cho BK, Knight EM, Lewis NE, Palsson BØ, Landick R. RNA Polymerase Mutants Found Through Adaptive Evolution Re-program Escherichia coli for Optimal Growth in Minimal Media. Proc Nat Acad Sci USA, (2010).
Portnoy VA, Scott DA, Lewis NE, Tarasova Y, Osterman A, Palsson BØ. Deletion of cytochrome oxidases and quinol monooxygenase blocks aerobic-anaerobic shift in Escherichia coli K-12 MG1655. Appl Environ Microbiol, (2010).
Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, Polpitiya AD, Adkins JN, Schramm G, Purvine SO, Lopez-Ferrer D, Weitz KK, Eils R, König R, Smith RD, Palsson BØ. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol 6:390 (2010).
Bar-Even A, Noor E, Lewis NE, Milo R. Design and Analysis of Synthetic Carbon Fixation Pathways. Proc Nat Acad Sci USA, (2010).
Lewis NE, Cho BK, Knight EM, and Palsson BO. Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content, Journal of Bacteriology, 191(11):3437-44, (2009).
Lewis NE, Jamshidi N, Thiele I, Palsson BO. Metabolic systems biology: a constraint-based approach. In "The Encyclopedia of Complexity and Systems Science."
Lewis NE, Thulin CD. Removal of Abundant Non-Informative Proteins from Blood Serum for Biomarker Discovery. ORCA - Journal of Undergraduate Research, (2006).
Merrell K, Southwick K, Graves SW, Esplin MS, Lewis NE, Thulin CD. Analysis of Low−Abundance, Low−Molecular−Weight Serum Proteins Using Mass Spectrometry. Journal of Biomolecular Techniques, 15, 238, (2004).
Posters and Talks
Lewis NE. "Bringing mechanisms into omics data through genome-scale modeling." Invited Talk at the IOMPA session of the International Conference on Systems Biology, August 2011, Heidelberg, Germany.
Lewis NE, Lee DH,, Conrad TM, Barrett CL, Schrimpe-Rultledge AC, Adkins JN, Smith RD, Palsson BO. "Integrating data and metabolic modeling shows that E. coli learns to grow optimally when evolved on a non-native carbon substrate." Poster at the International Conference on Systems Biology, August 2011, Heidelberg, Germany.
Lewis NE Draft Genome of CHO K1 plus a six-pack of additional CHO cell lines. Talk at the IBC Conference on Cell Line Development and Engineering 2011, Boston, MA
Lewis NE, Palsson BØ. “Predicting success of rewired metabolic networks.” Talk at the 2010 Plant Systems Biology Annual Training Grant Symposium, UCSD.
Lewis NE. “Increasing the value of high-throughput data through analysis in genome-scale models.” Invited talk at the 2010 CCSB Annual Retreat, Gloucester, Mass.
Lewis NE, Schramm G, Schellenberger J, Cheng J, Patel NK, Eils R, König R, Palsson BØ. “A large-scale model of human brain energy metabolism provides insight into the metabolic components of Alzheimer's Disease.” Talk at the 2010 Bioengineering Day, UCSD.
Lewis NE, Palsson BØ. “Predicting success of rewired metabolic networks.” Talk at the 2009 Plant Systems Biology Annual Training Grant Symposium, UCSD.
Lewis NE, Hixson KK, Conrad T, Charusanti P, Polpitiya AD, Smith RD, Palsson BØ. “Consistency of Omic Data with Computed Optimal Growth States from Genome-Scale Models” Poster at ICSB 2009, Stanford, CA.
Lewis NE, Palsson BØ, Segal E. “Investigating the Mechanisms of Transcriptional Timing in S. cerevisiae.” Poster at ISMB/ECCB 2009, Stockholm, Sweden.
Lewis NE, Cheng J, Patel N, Andersen MP, Lewis RA, Palsson BØ. “Constraints-based Modeling the neurochemistry of Alzheimer's disease.” Talk at the German Symposium on Systems Biology 2009, Heidelberg, Germany.
Lewis NE, Cheng J, Patel N, Messersmith MP, Lewis RA, Palsson BØ. “Modeling the neurochemistry of Alzheimer's disease: a constraints-based approach.” Talk at UCSD Interfaces Research Symposium 2008. Semi-finalist in abstract contest, and chosen as 1st place talk.
Lewis NE, Jobe T, Goswami S, Qutubuddin A, Briggs S, Palsson BØ. “Systems biology of the Arabidopsis chloroplast” Poster at IGERT 2008, Washington DC.
Lewis NE, Cheng J, Messersmith MP, Lewis RA, Palsson BO. “Multi-compartment models of brain metabolism provides insight into theories in neurochemistry.” Talk and poster at the Experimental Biology 2008.
Lewis NE, Cheng J, Messersmith MP, Palsson BØ. Talk at the 2008 All-grad research symposium.
Lewis NE, et al. “Comparison of Sample Preparation Methods for Serum Proteome Biomarker Discovery.” Presentation at the Conference for the Association of Biomolecular Resource Facilities 2006, Long Beach, CA. Semi−finalist in the poster contest.
Lewis NE, et al. “Methods in Analysis of the Blood Serum Proteome: Preparation for biomarker discovery.” Presentation at the BYU Spring Research Conference, March 2005.
Lewis NE, et al. “A survey of serum treatments for biomarker discovery.” Poster presented at the NIH, Aug 2004.
Merrell K, et al. “Analysis of Low−Abundance Serum Proteins Using Mass Spectrometry.” Presentation at the Conference for the Association of Biomolecular Resource Facilities. 2004, Portland, OR. Won the poster contest.
Contact Information
Email Address: n1lewis@ucsd.edu
Phone: (858) 822-1144
Mailing Address: 9500 Gilman Drive Mail Code 0412 La Jolla, CA 92093-0412
