Publications by authors named "Nathan E Lewis"

94Publications

In situ detection of protein interactions for recombinant therapeutic enzymes.

Biotechnol Bioeng 2020 Nov 10. Epub 2020 Nov 10.

Department of Pediatrics, University of California, San Diego, La Jolla, California, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/bit.27621DOI Listing
November 2020

Deciphering cell-cell interactions and communication from gene expression.

Nat Rev Genet 2020 Nov 9. Epub 2020 Nov 9.

Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41576-020-00292-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7649713PMC
November 2020

Systematically gap-filling the genome-scale metabolic model of CHO cells.

Biotechnol Lett 2020 Oct 10. Epub 2020 Oct 10.

Department of Bioengineering, University of California, San Diego, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10529-020-03021-wDOI Listing
October 2020

Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor.

Cell Host Microbe 2020 10 24;28(4):586-601.e6. Epub 2020 Aug 24.

Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, GA 30602, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.chom.2020.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7443692PMC
October 2020

Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor.

bioRxiv 2020 Jul 24. Epub 2020 Jul 24.

Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, Georgia, 30602, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/2020.06.25.172403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7386495PMC
July 2020

Increased Production of LIGHT by T Cells in Eosinophilic Esophagitis Promotes Differentiation of Esophageal Fibroblasts Toward an Inflammatory Phenotype.

Gastroenterology 2020 Nov 23;159(5):1778-1792.e13. Epub 2020 Jul 23.

Department of Pediatrics, University of California, San Diego, San Diego; Division of Allergy Immunology; Rady Children's Hospital, San Diego; Division of Gastroenterology, Department of Pediatrics, University of California, San Diego. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1053/j.gastro.2020.07.035DOI Listing
November 2020

What CHO is made of: Variations in the biomass composition of Chinese hamster ovary cell lines.

Metab Eng 2020 09 30;61:288-300. Epub 2020 Jun 30.

Acib - Austrian Centre of Industrial Biotechnology, 1190, Vienna, Austria; Department of Analytical Chemistry, University of Vienna, 1010, Vienna, Austria. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymben.2020.06.002DOI Listing
September 2020

StanDep: Capturing transcriptomic variability improves context-specific metabolic models.

PLoS Comput Biol 2020 05 12;16(5):e1007764. Epub 2020 May 12.

Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1007764DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7244210PMC
May 2020

Prenatal Origins of ASD: The When, What, and How of ASD Development.

Trends Neurosci 2020 05 15;43(5):326-342. Epub 2020 Apr 15.

Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA; Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tins.2020.03.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7373219PMC
May 2020

ZNF263 is a transcriptional regulator of heparin and heparan sulfate biosynthesis.

Proc Natl Acad Sci U S A 2020 04 10;117(17):9311-9317. Epub 2020 Apr 10.

Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093-0687;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1920880117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7196839PMC
April 2020

A metabolic network-based approach for developing feeding strategies for CHO cells to increase monoclonal antibody production.

Bioprocess Biosyst Eng 2020 Aug 24;43(8):1381-1389. Epub 2020 Mar 24.

Protein Chemistry and Proteomics Laboratory, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00449-020-02332-6DOI Listing
August 2020

From Genotype to Phenotype: Augmenting Deep Learning with Networks and Systems Biology.

Curr Opin Syst Biol 2019 Jun 4;15:68-73. Epub 2019 Apr 4.

Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.coisb.2019.04.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6880750PMC
June 2019

Assessing key decisions for transcriptomic data integration in biochemical networks.

PLoS Comput Biol 2019 07 19;15(7):e1007185. Epub 2019 Jul 19.

Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, California, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1007185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6668847PMC
July 2019

Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions.

PLoS Comput Biol 2019 04 15;15(4):e1006867. Epub 2019 Apr 15.

Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006867DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6483243PMC
April 2019

A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma.

Cell 2019 04 4;177(3):572-586.e22. Epub 2019 Apr 4.

Department of Pharmacology, University of California, San Diego School of Medicine, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA; Department of Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S00928674193027
Publisher Site
http://dx.doi.org/10.1016/j.cell.2019.03.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711371PMC
April 2019

Mitigating Clonal Variation in Recombinant Mammalian Cell Lines.

Trends Biotechnol 2019 09 18;37(9):931-942. Epub 2019 Mar 18.

The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Department of Biological Sciences, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tibtech.2019.02.007DOI Listing
September 2019

Systematic Evaluation of Site-Specific Recombinant Gene Expression for Programmable Mammalian Cell Engineering.

ACS Synth Biol 2019 04 12;8(4):758-774. Epub 2019 Mar 12.

The Novo Nordisk Foundation Center for Biosustainability , Technical University of Denmark , Kemitorvet, Building 220 , 2800 Kgs. Lyngby , Denmark.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acssynbio.8b00453DOI Listing
April 2019

Evolution of the exclusively human pathogen : Human-specific engagement of immunoregulatory Siglecs.

Evol Appl 2019 Feb 3;12(2):337-349. Epub 2019 Jan 3.

Glycobiology Research and Training Center University of California, San Diego La Jolla California.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/eva.12744DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346652PMC
February 2019

Revealing Key Determinants of Clonal Variation in Transgene Expression in Recombinant CHO Cells Using Targeted Genome Editing.

ACS Synth Biol 2018 12 14;7(12):2867-2878. Epub 2018 Nov 14.

The Novo Nordisk Foundation Center for Biosustainability , Technical University of Denmark , 2800 Kgs. Lyngby , Denmark.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acssynbio.8b00290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6535434PMC
December 2018

Minimizing Clonal Variation during Mammalian Cell Line Engineering for Improved Systems Biology Data Generation.

ACS Synth Biol 2018 09 16;7(9):2148-2159. Epub 2018 Aug 16.

The Novo Nordisk Foundation Center for Biosustainability , Technical University of Denmark , 2800 Kgs. Lyngby , Denmark.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/10.1021/acssynbio.8b00140
Publisher Site
http://dx.doi.org/10.1021/acssynbio.8b00140DOI Listing
September 2018

The ASD Living Biology: from cell proliferation to clinical phenotype.

Mol Psychiatry 2019 01 22;24(1):88-107. Epub 2018 Jun 22.

Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41380-018-0056-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309606PMC
January 2019

The emerging role of systems biology for engineering protein production in CHO cells.

Curr Opin Biotechnol 2018 06 7;51:64-69. Epub 2017 Dec 7.

Department of Bioengineering, University of California, San Diego, United States; Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, United States; Department of Pediatrics, University of California, San Diego, United States. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.copbio.2017.11.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988649PMC
June 2018

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens.

Sci Rep 2017 Nov 20;7(1):15854. Epub 2017 Nov 20.

Division of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-017-16193-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5696473PMC
November 2017

The Emerging Facets of Non-Cancerous Warburg Effect.

Front Endocrinol (Lausanne) 2017 23;8:279. Epub 2017 Oct 23.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Centre (CBRC), Thuwal, Saudi Arabia.

View Article

Download full-text PDF

Source
http://journal.frontiersin.org/article/10.3389/fendo.2017.00
Publisher Site
http://dx.doi.org/10.3389/fendo.2017.00279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5660072PMC
October 2017

Improvements in protein production in mammalian cells from targeted metabolic engineering.

Curr Opin Syst Biol 2017 Dec 6;6:1-6. Epub 2017 Jun 6.

Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.coisb.2017.05.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5663301PMC
December 2017

Hierarchical cortical transcriptome disorganization in autism.

Mol Autism 2017 21;8:29. Epub 2017 Jun 21.

Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California, San Diego, La Jolla, CA USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13229-017-0147-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5480153PMC
March 2018

Human milk oligosaccharide composition predicts risk of necrotising enterocolitis in preterm infants.

Gut 2018 06 5;67(6):1064-1070. Epub 2017 Apr 5.

Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA.

View Article

Download full-text PDF

Source
http://gut.bmj.com/lookup/doi/10.1136/gutjnl-2016-312819
Publisher Site
http://dx.doi.org/10.1136/gutjnl-2016-312819DOI Listing
June 2018

A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models.

Cell Syst 2017 03 15;4(3):318-329.e6. Epub 2017 Feb 15.

Novo Nordisk Foundation Center for Biosustainability at UC San Diego, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cels.2017.01.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5526624PMC
March 2017

Ribosome profiling-guided depletion of an mRNA increases cell growth rate and protein secretion.

Sci Rep 2017 01 16;7:40388. Epub 2017 Jan 16.

Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep40388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5238448PMC
January 2017

Predictive glycoengineering of biosimilars using a Markov chain glycosylation model.

Biotechnol J 2017 Feb 28;12(2). Epub 2016 Dec 28.

Department of Pediatrics, University of California San Diego, School of Medicine, La Jolla, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/biot.201600489DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5293603PMC
February 2017

Modulating carbohydrate-protein interactions through glycoengineering of monoclonal antibodies to impact cancer physiology.

Curr Opin Struct Biol 2016 10 14;40:104-111. Epub 2016 Sep 14.

Department of Pediatrics, University of California, San Diego, CA, USA; The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, CA, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.sbi.2016.08.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161599PMC
October 2016

Recon 2.2: from reconstruction to model of human metabolism.

Metabolomics 2016;12:109. Epub 2016 Jun 7.

Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK ; School of Computer Science, The University of Manchester, Manchester, M13 9PL UK ; Center for Quantitative Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030-6033 USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11306-016-1051-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896983PMC
June 2016

Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis.

Genome Med 2016 Mar 31;8(1):34. Epub 2016 Mar 31.

Molecular Biosciences and Bioengineering Graduate Program, University of Hawaii at Manoa, Honolulu, HI, 96822, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13073-016-0289-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4818393PMC
March 2016

Quantitative feature extraction from the Chinese hamster ovary bioprocess bibliome using a novel meta-analysis workflow.

Biotechnol Adv 2016 Sep-Oct;34(5):621-633. Epub 2016 Mar 3.

Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, San Diego, CA, USA; Department of Pediatrics, University of California, San Diego, CA, USA; The Jacobs School of Engineering CHO Systems Biology Center, University of California, San Diego, CA, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.biotechadv.2016.02.011DOI Listing
December 2017

A Markov chain model for N-linked protein glycosylation--towards a low-parameter tool for model-driven glycoengineering.

Metab Eng 2016 Jan 29;33:52-66. Epub 2015 Oct 29.

Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States; The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA 92093, United States. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymben.2015.10.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5031499PMC
January 2016

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.

Nucleic Acids Res 2016 Jan 17;44(D1):D515-22. Epub 2015 Oct 17.

Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA 92093, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkv1049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702785PMC
January 2016

Elucidation of the CHO Super-Ome (CHO-SO) by Proteoinformatics.

J Proteome Res 2015 Nov 13;14(11):4687-703. Epub 2015 Oct 13.

Department of Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jproteome.5b00588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4721571PMC
November 2015

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.

PLoS Comput Biol 2015 Aug 27;11(8):e1004321. Epub 2015 Aug 27.

Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America; Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1004321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4552468PMC
August 2015

Systems analysis of host-parasite interactions.

Wiley Interdiscip Rev Syst Biol Med 2015 Nov-Dec;7(6):381-400. Epub 2015 Aug 26.

Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/wsbm.1311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679367PMC
July 2016

Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling.

Biotechnol J 2015 Jul 23;10(7):939-49. Epub 2015 Jun 23.

Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego School of Medicine, San Diego, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/biot.201400647DOI Listing
July 2015

CRISPR/Cas9-mediated genome engineering of CHO cell factories: Application and perspectives.

Biotechnol J 2015 Jul 9;10(7):979-94. Epub 2015 Jun 9.

The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/biot.201500082DOI Listing
July 2015

Rapid neurogenesis through transcriptional activation in human stem cells.

Mol Syst Biol 2014 Nov 17;10:760. Epub 2014 Nov 17.

Department of Genetics, Harvard Medical School, Boston, MA, USA Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299601PMC
http://dx.doi.org/10.15252/msb.20145508DOI Listing
November 2014

Systems glycobiology for glycoengineering.

Curr Opin Biotechnol 2014 Dec 7;30:218-24. Epub 2014 Sep 7.

Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, United States. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.copbio.2014.08.004DOI Listing
December 2014

Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice.

PLoS One 2014 16;9(7):e102319. Epub 2014 Jul 16.

Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102319PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4100879PMC
November 2015

Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

Mol Syst Biol 2014 Jul 1;10:737. Epub 2014 Jul 1.

Department of Bioengineering, University of California San Diego, La Jolla, CA, USA Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299494PMC
http://dx.doi.org/10.15252/msb.20145243DOI Listing
July 2014

The role of replicates for error mitigation in next-generation sequencing.

Nat Rev Genet 2014 01 10;15(1):56-62. Epub 2013 Dec 10.

Department of Genetics, Harvard Medical School, and the Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nrg3655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103745PMC
January 2014

The evolution of genome-scale models of cancer metabolism.

Front Physiol 2013 Sep 3;4:237. Epub 2013 Sep 3.

Department of Biology, Brigham Young University Provo, UT, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fphys.2013.00237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759783PMC
September 2013

The emerging CHO systems biology era: harnessing the 'omics revolution for biotechnology.

Curr Opin Biotechnol 2013 Dec 20;24(6):1102-7. Epub 2013 Mar 20.

Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.copbio.2013.02.007DOI Listing
December 2013

Analysis of omics data with genome-scale models of metabolism.

Mol Biosyst 2013 Feb 18;9(2):167-74. Epub 2012 Dec 18.

Department of Bioengineering, University of California - San Diego, La Jolla, CA 92093-0412, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/c2mb25453kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3594511PMC
February 2013

A proof for loop-law constraints in stoichiometric metabolic networks.

BMC Syst Biol 2012 Nov 12;6:140. Epub 2012 Nov 12.

Department of Plant Sciences, 234 Herzl St., Weizmann Institute of Science, Rehovot 76100, Israel.

View Article

Download full-text PDF

Source
http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
Publisher Site
http://dx.doi.org/10.1186/1752-0509-6-140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3560238PMC
November 2012

Network context and selection in the evolution to enzyme specificity.

Science 2012 Aug;337(6098):1101-4

Department of Bioengineering, University of California San Diego, La Jolla, CA 92093-0412, USA.

View Article

Download full-text PDF

Source
http://www.sciencemag.org/cgi/doi/10.1126/science.1216861
Publisher Site
http://dx.doi.org/10.1126/science.1216861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3536066PMC
August 2012

In silico method for modelling metabolism and gene product expression at genome scale.

Nat Commun 2012 Jul 3;3:929. Epub 2012 Jul 3.

Department of Bioengineering, University of California-San Diego, PFBH Room 419, 9500 Gliman Drive, La Jolla, California 92093-0412, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms1928DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827721PMC
July 2012

Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.

Nat Rev Microbiol 2012 Feb 27;10(4):291-305. Epub 2012 Feb 27.

Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nrmicro2737DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3536058PMC
February 2012

Microbial laboratory evolution in the era of genome-scale science.

Mol Syst Biol 2011 Jul 5;7:509. Epub 2011 Jul 5.

Department of Bioengineering, University of California San Diego, La Jolla, CA 92093-0412, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/msb.2011.42DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159978PMC
July 2011

The role of cellular objectives and selective pressures in metabolic pathway evolution.

Curr Opin Biotechnol 2011 Aug 12;22(4):595-600. Epub 2011 Apr 12.

Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.copbio.2011.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173765PMC
August 2011

Elimination of thermodynamically infeasible loops in steady-state metabolic models.

Biophys J 2011 Feb;100(3):544-553

Bioengineering Department, University of California, San Diego, California. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bpj.2010.12.3707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030201PMC
February 2011

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media.

Proc Natl Acad Sci U S A 2010 Nov 5;107(47):20500-5. Epub 2010 Nov 5.

Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093-0412, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0911253107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996682PMC
November 2010

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.

Mol Syst Biol 2010 Oct;6:422

Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall, La Jolla, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/msb.2010.68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990636PMC
October 2010

Design and analysis of synthetic carbon fixation pathways.

Proc Natl Acad Sci U S A 2010 May 21;107(19):8889-94. Epub 2010 Apr 21.

Departments of Plant Sciences and Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot 76100, Israel.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0907176107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889323PMC
May 2010

Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content.

J Bacteriol 2009 Jun 10;191(11):3437-44. Epub 2009 Apr 10.

Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0412, La Jolla, CA 92093-0412, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/JB.00034-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2681886PMC
June 2009

Analysis of low-abundance, low-molecular-weight serum proteins using mass spectrometry.

J Biomol Tech 2004 Dec;15(4):238-48

Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2291707PMC
December 2004