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List of works by Nathan E. Lewis

A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.

scientific article published on November 2016

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

scientific article published on 29 October 2015

A Markov model of glycosylation elucidates isozyme specificity and glycosyltransferase interactions for glycoengineering

scientific article published on 23 January 2020

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

scientific article published on 14 February 2017

A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

scientific article published on 27 October 2020

A novel low-parameter computational model to aid in-silico glycoengineering.

scientific article

A perturbed gene network containing PI3K-AKT, RAS-ERK and WNT-β-catenin pathways in leukocytes is linked to ASD genetics and symptom severity

scientific article published on 23 September 2019

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

scientific article

A reference genome of the Chinese hamster based on a hybrid assembly strategy

article

An enhanced CRISPR repressor for targeted mammalian gene regulation

scientific article published on 16 July 2018

Analysis of omics data with genome-scale models of metabolism

scientific article

Assessing key decisions for transcriptomic data integration in biochemical networks

scientific article published on 19 July 2019

Awakening dormant glycosyltransferases in CHO cells with CRISPRa

scientific article published on 12 November 2019

Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity

scientific article published on 18 August 2020

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

scientific article

CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines

scientific article published on 22 December 2020

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

scientific article published on 09 June 2015

Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers

scientific article published on 14 December 2015

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

article published in the Proceedings of the National Academy of Sciences of the United States of America

Combating viral contaminants in CHO cells by engineering innate immunity.

scientific article published on 20 June 2019

Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.

scientific article

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

scientific article

Correcting for sparsity and interdependence in glycomics by accounting for glycan biosynthesis

scientific article published on 17 August 2021

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

scientific article published on 01 March 2019

Deciphering cell-cell interactions and communication from gene expression

scientific article published on 09 November 2020

Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655.

scientific article

Design and analysis of synthetic carbon fixation pathways

scientific article

Dietary serine-microbiota interaction enhances chemotherapeutic toxicity without altering drug conversion

scientific article published on 22 May 2020

Do genome-scale models need exact solvers or clearer standards?

scientific article published on 14 October 2015

Dual RNA-seq identifies human mucosal immunity protein Mucin-13 as a hallmark of Plasmodium exoerythrocytic infection

scientific article published in Nature Communications

Elimination of thermodynamically infeasible loops in steady-state metabolic models

scientific article

Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multi-omics integration

scientific article published on 04 May 2022

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

scientific article

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting

scientific article published on 4 January 2018

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

scientific article published on 10 April 2009

Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion

Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion

scientific article published on 02 January 2020

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

scientific article

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

scientific article

ImmCellFie: A user-friendly web-based platform to infer metabolic function from omics data

scientific article published in 2023

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

scientific article published on 03 July 2012

In situ detection of protein interactions for recombinant therapeutic enzymes

scientific article published on 10 November 2020

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

scientific article published on 23 July 2020

Increased mAb production in amplified CHO cell lines is associated with increased interaction of CREB1 with transgene promoter

scientific article published on 05 October 2019

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

scientific article published on 15 April 2019

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

scientific article

JSBML 1.0: providing a smorgasbord of options to encode systems biology models

scientific article

Large-scale associations between the leukocyte transcriptome and BOLD responses to speech differ in autism early language outcome subtypes

scientific article published on 26 November 2018

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

scientific article

List of Contributors

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Microbial laboratory evolution in the era of genome-scale science

scientific article

Minimal metabolic pathway structure is consistent with associated biomolecular interactions

scientific article

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

scientific article published on 16 August 2018

Mitigating Clonal Variation in Recombinant Mammalian Cell Lines

scientific article published on 18 March 2019

Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism ⬇️

article

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

scientific article published on 14 September 2016

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

scientific article

Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing

scientific article published on 21 January 2021

Multiplex secretome engineering enhances recombinant protein production and purity

scientific article published on 20 April 2020

Network context and selection in the evolution to enzyme specificity.

scientific article

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

scientific article published on 31 March 2016

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

scientific article

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

scientific article published on 23 June 2015

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

scientific article

Predictive glycoengineering of biosimilars using a Markov chain glycosylation model.

scientific article published on 17 November 2016

Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements

scientific article published on 08 May 2019

Proteomic analysis of Chinese hamster ovary cells

scientific article published on 05 October 2012

Proteomic atlas of organ vasculopathies triggered by Staphylococcus aureus sepsis

scientific article published on 11 October 2019

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

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

scientific article published on 3 March 2016

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

scientific article (publication date: 4 August 2011)

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

scientific article

Rapid neurogenesis through transcriptional activation in human stem cells.

scientific article

Recon 2.2: from reconstruction to model of human metabolism ⬇️

scientific article

Reduced apoptosis in Chinese hamster ovary cells via optimized CRISPR interference

scientific article published on 02 April 2019

Revealing key determinants of clonal variation in transgene expression in recombinant CHO cells using targeted genome editing

scientific article published on 14 November 2018

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

scientific article published on 16 January 2017

StanDep: Capturing transcriptomic variability improves context-specific metabolic models

scientific article published on 12 May 2020

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

scientific article published on 12 March 2019

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

scientific article published on 10 October 2020

Systems analysis of host-parasite interactions

scientific article

Systems glycobiology for glycoengineering

scientific article published on 07 September 2014

The ASD Living Biology: from cell proliferation to clinical phenotype

scientific article published on 22 June 2018

The Emerging Facets of Non-Cancerous Warburg Effect.

scientific article published on 23 October 2017

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

scientific article

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

scientific article published on 6 December 2017

The evolution of genome-scale models of cancer metabolism

scientific article published in 2013

The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line

scientific article

The lytic polysaccharide monooxygenase CbpD promotes Pseudomonas aeruginosa virulence in systemic infection

scientific article published on 23 February 2021

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

scientific article

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

scientific article

Type 2 Immunity and Age Modify Gene Expression of COVID19 Receptors in Eosinophilic Gastrointestinal Disorders

scientific article published on 23 December 2020

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

preprint published on 24 July 2020

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

scientific article published on 24 August 2020

What are housekeeping genes?

scientific article published on 13 July 2022

Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion

scientific article (publication date: 10 January 2017)

WormJam: A consensus C. elegans Metabolic Reconstruction and Metabolomics Community and Workshop Series

scientific article published on 6 September 2017

ZNF263 is a transcriptional regulator of heparin and heparan sulfate biosynthesis

scientific article published on 10 April 2020

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