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Items: 1 to 50 of 68

1.

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

Landig CS, Hazel A, Kellman BP, Fong JJ, Schwarz F, Agarwal S, Varki N, Massari P, Lewis NE, Ram S, Varki A.

Evol Appl. 2019 Jan 3;12(2):337-349. doi: 10.1111/eva.12744. eCollection 2019 Feb.

2.

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

Witting M, Hastings J, Rodriguez N, Joshi CJ, Hattwell JPN, Ebert PR, van Weeghel M, Gao AW, Wakelam MJO, Houtkooper RH, Mains A, Le Novère N, Sadykoff S, Schroeder F, Lewis NE, Schirra HJ, Kaleta C, Casanueva O.

Front Mol Biosci. 2018 Nov 14;5:96. doi: 10.3389/fmolb.2018.00096. eCollection 2018.

3.

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

Lombardo MV, Pramparo T, Gazestani V, Warrier V, Bethlehem RAI, Carter Barnes C, Lopez L, Lewis NE, Eyler L, Pierce K, Courchesne E.

Nat Neurosci. 2018 Dec;21(12):1680-1688. doi: 10.1038/s41593-018-0281-3. Epub 2018 Nov 26.

PMID:
30482947
4.

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

Lee JS, Park JH, Ha TK, Samoudi M, Lewis NE, Palsson BO, Kildegaard HF, Lee GM.

ACS Synth Biol. 2018 Nov 14. doi: 10.1021/acssynbio.8b00290. [Epub ahead of print]

PMID:
30388888
5.

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow.

Brunk E, Chang RL, Xia J, Hefzi H, Yurkovich JT, Kim D, Buckmiller E, Wang HH, Cho BK, Yang C, Palsson BO, Church GM, Lewis NE.

Proc Natl Acad Sci U S A. 2018 Oct 23;115(43):11096-11101. doi: 10.1073/pnas.1811971115. Epub 2018 Oct 9.

PMID:
30301795
6.

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

Grav LM, Sergeeva D, Lee JS, Marin de Mas I, Lewis NE, Andersen MR, Nielsen LK, Lee GM, Kildegaard HF.

ACS Synth Biol. 2018 Sep 21;7(9):2148-2159. doi: 10.1021/acssynbio.8b00140. Epub 2018 Aug 16.

PMID:
30060646
7.

An enhanced CRISPR repressor for targeted mammalian gene regulation.

Yeo NC, Chavez A, Lance-Byrne A, Chan Y, Menn D, Milanova D, Kuo CC, Guo X, Sharma S, Tung A, Cecchi RJ, Tuttle M, Pradhan S, Lim ET, Davidsohn N, Ebrahimkhani MR, Collins JJ, Lewis NE, Kiani S, Church GM.

Nat Methods. 2018 Aug;15(8):611-616. doi: 10.1038/s41592-018-0048-5. Epub 2018 Jul 16.

8.

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

Courchesne E, Pramparo T, Gazestani VH, Lombardo MV, Pierce K, Lewis NE.

Mol Psychiatry. 2019 Jan;24(1):88-107. doi: 10.1038/s41380-018-0056-y. Epub 2018 Jun 22. Review.

9.

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

Rupp O, MacDonald ML, Li S, Dhiman H, Polson S, Griep S, Heffner K, Hernandez I, Brinkrolf K, Jadhav V, Samoudi M, Hao H, Kingham B, Goesmann A, Betenbaugh MJ, Lewis NE, Borth N, Lee KH.

Biotechnol Bioeng. 2018 Aug;115(8):2087-2100. doi: 10.1002/bit.26722. Epub 2018 May 29.

10.

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

Abdel-Haleem AM, Hefzi H, Mineta K, Gao X, Gojobori T, Palsson BO, Lewis NE, Jamshidi N.

PLoS Comput Biol. 2018 Jan 4;14(1):e1005895. doi: 10.1371/journal.pcbi.1005895. eCollection 2018 Jan.

11.

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

Kuo CC, Chiang AW, Shamie I, Samoudi M, Gutierrez JM, Lewis NE.

Curr Opin Biotechnol. 2018 Jun;51:64-69. doi: 10.1016/j.copbio.2017.11.015. Epub 2017 Dec 7. Review.

PMID:
29223005
12.

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

Spahn PN, Bath T, Weiss RJ, Kim J, Esko JD, Lewis NE, Harismendy O.

Sci Rep. 2017 Nov 20;7(1):15854. doi: 10.1038/s41598-017-16193-9.

13.

The Emerging Facets of Non-Cancerous Warburg Effect.

Abdel-Haleem AM, Lewis NE, Jamshidi N, Mineta K, Gao X, Gojobori T.

Front Endocrinol (Lausanne). 2017 Oct 23;8:279. doi: 10.3389/fendo.2017.00279. eCollection 2017.

14.

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

Richelle A, Lewis NE.

Curr Opin Syst Biol. 2017 Dec;6:1-6. doi: 10.1016/j.coisb.2017.05.019. Epub 2017 Jun 6.

15.

Hierarchical cortical transcriptome disorganization in autism.

Lombardo MV, Courchesne E, Lewis NE, Pramparo T.

Mol Autism. 2017 Jun 21;8:29. doi: 10.1186/s13229-017-0147-7. eCollection 2017.

16.

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

Autran CA, Kellman BP, Kim JH, Asztalos E, Blood AB, Spence ECH, Patel AL, Hou J, Lewis NE, Bode L.

Gut. 2018 Jun;67(6):1064-1070. doi: 10.1136/gutjnl-2016-312819. Epub 2017 Apr 5.

PMID:
28381523
17.

Placental Pathologic Features in Fetomaternal Hemorrhage Detected By Flow Cytometry.

Lewis NE, Marszalek L, Ernst LM.

Pediatr Dev Pathol. 2017 Mar-Apr;20(2):142-151. doi: 10.1177/1093526616687652. Epub 2017 Feb 8.

PMID:
28326960
18.

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

Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P.

Nat Methods. 2017 Jun;14(6):573-576. doi: 10.1038/nmeth.4225. Epub 2017 Mar 20.

19.

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

Opdam S, Richelle A, Kellman B, Li S, Zielinski DC, Lewis NE.

Cell Syst. 2017 Mar 22;4(3):318-329.e6. doi: 10.1016/j.cels.2017.01.010. Epub 2017 Feb 15.

20.

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

Kallehauge TB, Li S, Pedersen LE, Ha TK, Ley D, Andersen MR, Kildegaard HF, Lee GM, Lewis NE.

Sci Rep. 2017 Jan 16;7:40388. doi: 10.1038/srep40388.

21.

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

van Wijk XM, Döhrmann S, Hallström BM, Li S, Voldborg BG, Meng BX, McKee KK, van Kuppevelt TH, Yurchenco PD, Palsson BO, Lewis NE, Nizet V, Esko JD.

MBio. 2017 Jan 10;8(1). pii: e02128-16. doi: 10.1128/mBio.02128-16.

22.

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

Hefzi H, Ang KS, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D, Martinez VS, Kyriakopoulos S, Jiménez NE, Zielinski DC, Quek LE, Wulff T, Arnsdorf J, Li S, Lee JS, Paglia G, Loira N, Spahn PN, Pedersen LE, Gutierrez JM, King ZA, Lund AM, Nagarajan H, Thomas A, Abdel-Haleem AM, Zanghellini J, Kildegaard HF, Voldborg BG, Gerdtzen ZP, Betenbaugh MJ, Palsson BO, Andersen MR, Nielsen LK, Borth N, Lee DY, Lewis NE.

Cell Syst. 2016 Nov 23;3(5):434-443.e8. doi: 10.1016/j.cels.2016.10.020.

23.

Predictive glycoengineering of biosimilars using a Markov chain glycosylation model.

Spahn PN, Hansen AH, Kol S, Voldborg BG, Lewis NE.

Biotechnol J. 2017 Feb;12(2). doi: 10.1002/biot.201600489. Epub 2016 Dec 28.

24.

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

Chiang AW, Li S, Spahn PN, Richelle A, Kuo CC, Samoudi M, Lewis NE.

Curr Opin Struct Biol. 2016 Oct;40:104-111. doi: 10.1016/j.sbi.2016.08.008. Epub 2016 Sep 14. Review.

25.

Improving the Efficiency and Ease of Healthcare Analysis Through Use of Data Visualization Dashboards.

Stadler JG, Donlon K, Siewert JD, Franken T, Lewis NE.

Big Data. 2016 Jun;4(2):129-35. doi: 10.1089/big.2015.0059.

PMID:
27441717
26.

Recon 2.2: from reconstruction to model of human metabolism.

Swainston N, Smallbone K, Hefzi H, Dobson PD, Brewer J, Hanscho M, Zielinski DC, Ang KS, Gardiner NJ, Gutierrez JM, Kyriakopoulos S, Lakshmanan M, Li S, Liu JK, Martínez VS, Orellana CA, Quek LE, Thomas A, Zanghellini J, Borth N, Lee DY, Nielsen LK, Kell DB, Lewis NE, Mendes P.

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

27.

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

Huang S, Chong N, Lewis NE, Jia W, Xie G, Garmire LX.

Genome Med. 2016 Mar 31;8(1):34. doi: 10.1186/s13073-016-0289-9.

28.

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

Golabgir A, Gutierrez JM, Hefzi H, Li S, Palsson BO, Herwig C, Lewis NE.

Biotechnol Adv. 2016 Sep-Oct;34(5):621-633. doi: 10.1016/j.biotechadv.2016.02.011. Epub 2016 Mar 3. Review.

PMID:
26948029
29.

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

Spahn PN, Hansen AH, Hansen HG, Arnsdorf J, Kildegaard HF, Lewis NE.

Metab Eng. 2016 Jan;33:52-66. doi: 10.1016/j.ymben.2015.10.007. Epub 2015 Oct 29.

30.

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

King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE.

Nucleic Acids Res. 2016 Jan 4;44(D1):D515-22. doi: 10.1093/nar/gkv1049. Epub 2015 Oct 17.

31.

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

Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.

32.

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

Kumar A, Baycin-Hizal D, Wolozny D, Pedersen LE, Lewis NE, Heffner K, Chaerkady R, Cole RN, Shiloach J, Zhang H, Bowen MA, Betenbaugh MJ.

J Proteome Res. 2015 Nov 6;14(11):4687-703. doi: 10.1021/acs.jproteome.5b00588. Epub 2015 Oct 13.

33.

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

King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO.

PLoS Comput Biol. 2015 Aug 27;11(8):e1004321. doi: 10.1371/journal.pcbi.1004321. eCollection 2015 Aug.

34.

Systems analysis of host-parasite interactions.

Swann J, Jamshidi N, Lewis NE, Winzeler EA.

Wiley Interdiscip Rev Syst Biol Med. 2015 Nov-Dec;7(6):381-400. doi: 10.1002/wsbm.1311. Epub 2015 Aug 26. Review.

35.

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

Gutierrez JM, Lewis NE.

Biotechnol J. 2015 Jul;10(7):939-49. doi: 10.1002/biot.201400647. Epub 2015 Jun 23. Review.

PMID:
26099571
36.

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

Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F, Netz E, Diamantikos A, Eichner J, Keller R, Wrzodek C, Fröhlich S, Lewis NE, Myers CJ, Le Novère N, Palsson BØ, Hucka M, Dräger A.

Bioinformatics. 2015 Oct 15;31(20):3383-6. doi: 10.1093/bioinformatics/btv341. Epub 2015 Jun 16.

37.

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

Lee JS, Grav LM, Lewis NE, Faustrup Kildegaard H.

Biotechnol J. 2015 Jul;10(7):979-94. doi: 10.1002/biot.201500082. Epub 2015 Jun 9. Review.

PMID:
26058577
38.

Rapid neurogenesis through transcriptional activation in human stem cells.

Busskamp V, Lewis NE, Guye P, Ng AH, Shipman SL, Byrne SM, Sanjana NE, Murn J, Li Y, Li S, Stadler M, Weiss R, Church GM.

Mol Syst Biol. 2014 Nov 17;10:760. doi: 10.15252/msb.20145508.

39.

Breaking the bacterial protein targeting and translocation model: oral organisms as a case in point.

Lewis NE, Brady LJ.

Mol Oral Microbiol. 2015 Jun;30(3):186-97. doi: 10.1111/omi.12088. Epub 2014 Dec 26. Review.

40.

Systems glycobiology for glycoengineering.

Spahn PN, Lewis NE.

Curr Opin Biotechnol. 2014 Dec;30:218-24. doi: 10.1016/j.copbio.2014.08.004. Epub 2014 Sep 7. Review.

PMID:
25202878
41.

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

Kumar A, Harrelson T, Lewis NE, Gallagher EJ, LeRoith D, Shiloach J, Betenbaugh MJ.

PLoS One. 2014 Jul 16;9(7):e102319. doi: 10.1371/journal.pone.0102319. eCollection 2014.

42.

Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO.

Mol Syst Biol. 2014 Jul 1;10:737. doi: 10.15252/msb.20145243.

43.

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

Robasky K, Lewis NE, Church GM.

Nat Rev Genet. 2014 Jan;15(1):56-62. doi: 10.1038/nrg3655. Epub 2013 Dec 10. Review.

44.

The evolution of genome-scale models of cancer metabolism.

Lewis NE, Abdel-Haleem AM.

Front Physiol. 2013 Sep 3;4:237. doi: 10.3389/fphys.2013.00237. Review.

45.

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

Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C, Xie M, Chen W, Li N, Baycin-Hizal D, Latif H, Forster J, Betenbaugh MJ, Famili I, Xu X, Wang J, Palsson BO.

Nat Biotechnol. 2013 Aug;31(8):759-65. doi: 10.1038/nbt.2624. Epub 2013 Jul 21.

PMID:
23873082
46.

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

Kildegaard HF, Baycin-Hizal D, Lewis NE, Betenbaugh MJ.

Curr Opin Biotechnol. 2013 Dec;24(6):1102-7. doi: 10.1016/j.copbio.2013.02.007. Epub 2013 Mar 20. Review.

PMID:
23523260
47.

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

Hyduke DR, Lewis NE, Palsson BØ.

Mol Biosyst. 2013 Feb 2;9(2):167-74. doi: 10.1039/c2mb25453k. Epub 2012 Dec 18. Review.

48.

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

Noor E, Lewis NE, Milo R.

BMC Syst Biol. 2012 Nov 12;6:140. doi: 10.1186/1752-0509-6-140.

49.

Proteomic analysis of Chinese hamster ovary cells.

Baycin-Hizal D, Tabb DL, Chaerkady R, Chen L, Lewis NE, Nagarajan H, Sarkaria V, Kumar A, Wolozny D, Colao J, Jacobson E, Tian Y, O'Meally RN, Krag SS, Cole RN, Palsson BO, Zhang H, Betenbaugh M.

J Proteome Res. 2012 Nov 2;11(11):5265-76. doi: 10.1021/pr300476w. Epub 2012 Oct 5.

50.

Network context and selection in the evolution to enzyme specificity.

Nam H, Lewis NE, Lerman JA, Lee DH, Chang RL, Kim D, Palsson BO.

Science. 2012 Aug 31;337(6098):1101-4. doi: 10.1126/science.1216861.

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