| Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2. 0 J Schellenberger, R Que, RMT Fleming, I Thiele, JD Orth, AM Feist, ... Nature protocols 6 (9), 1290-1307, 2011 | 1676 | 2011 |
| Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3. 0 L Heirendt, S Arreckx, T Pfau, SN Mendoza, A Richelle, A Heinken, ... Nature Protocols 14, 639–702, 2019 | 1136 | 2019 |
| The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line X Xu*, H Nagarajan*, NE Lewis*, S Pan*, Z Cai*, X Liu, W Chen, M Xie, ... Nature biotechnology 29 (8), 735, 2011 | 991 | 2011 |
| BiGG Models: A platform for integrating, standardizing and sharing genome-scale models ZA King, J Lu, A Dräger, P Miller, S Federowicz, JA Lerman, A Ebrahim, ... Nucleic acids research 44 (D1), D515-D522, 2016 | 967 | 2016 |
| Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods NE Lewis, H Nagarajan, BO Palsson Nature Reviews Microbiology 10 (4), 291-305, 2012 | 957 | 2012 |
| Deciphering cell–cell interactions and communication from gene expression E Armingol, A Officer, O Harismendy, NE Lewis Nature Reviews Genetics 22 (2), 71-88, 2021 | 915 | 2021 |
| Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models NE Lewis, KK Hixson, TM Conrad, JA Lerman, P Charusanti, AD Polpitiya, ... Molecular systems biology 6 (1), 390, 2010 | 837 | 2010 |
| Design and analysis of synthetic carbon fixation pathways A Bar-Even, E Noor, NE Lewis, R Milo Proceedings of the National Academy of Sciences 107 (19), 8889-8894, 2010 | 597 | 2010 |
| An enhanced CRISPR repressor for targeted mammalian gene regulation NC Yeo, A Chavez, A Lance-Byrne, Y Chan, D Menn, D Milanova, ... Nature methods 15 (8), 611-616, 2018 | 491 | 2018 |
| Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome NE Lewis*, X Liu*, Y Li*, H Nagarajan*, G Yerganian, E O'brien, ... Nature biotechnology 31 (8), 759, 2013 | 466 | 2013 |
| MEMOTE for standardized genome-scale metabolic model testing C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ... Nature biotechnology 38 (3), 272-276, 2020 | 455* | 2020 |
| Virus-receptor interactions of glycosylated SARS-CoV-2 spike and human ACE2 receptor P Zhao, JL Praissman, OC Grant, Y Cai, T Xiao, KE Rosenbalm, K Aoki, ... Cell host & microbe 28 (4), 586-601. e6, 2020 | 439 | 2020 |
| Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways ZA King, A Dräger, A Ebrahim, N Sonnenschein, NE Lewis, BO Palsson PLoS computational biology 11 (8), e1004321, 2015 | 407 | 2015 |
| Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactions JP Shen, D Zhao, R Sasik, J Luebeck, A Birmingham, ... Nature methods 14 (6), 573-576, 2017 | 387 | 2017 |
| The role of replicates for error mitigation in next-generation sequencing K Robasky*, NE Lewis*, GM Church Nature Reviews Genetics 15 (1), 56, 2014 | 366 | 2014 |
| In silico method for modelling metabolism and gene product expression at genome scale JA Lerman, DR Hyduke, H Latif, VA Portnoy, NE Lewis, JD Orth, ... Nature communications 3 (1), 929, 2012 | 358 | 2012 |
| Microbial laboratory evolution in the era of genome‐scale science TM Conrad, NE Lewis, BØ Palsson Molecular systems biology 7 (1), 509, 2011 | 354 | 2011 |
| Recon 2.2: from reconstruction to model of human metabolism N Swainston, K Smallbone, H Hefzi, PD Dobson, J Brewer, M Hanscho, ... Metabolomics 12, 1-7, 2016 | 330 | 2016 |
| Network context and selection in the evolution to enzyme specificity H Nam*, NE Lewis*, JA Lerman, DH Lee, RL Chang, D Kim, BO Palsson Science 337 (6098), 1101-1104, 2012 | 315 | 2012 |
| Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions A Bordbar, NE Lewis, J Schellenberger, BØ Palsson, N Jamshidi Molecular systems biology 6 (1), 422, 2010 | 315 | 2010 |
Bernhard PalssonBioengineering and Pediatrics, UC-San DiegoVerified email at ucsd.edu
