Nathan Lewis

Title(s)Professor In Residence, Pediatrics
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Research Activities and Funding
    ImmCellFIE: producing high-resolution snapshots of the functions of immune cells
    NIH UH2AI153029Jun 22, 2020 - May 31, 2022
    Role: Principal Investigator
    Developmental Functional Genomics in ASD Toddlers
    NIH R01MH110558Sep 1, 2016 - Jun 30, 2021
    Role: Principal Investigator
    Unraveling the mammalian secretory pathway through systems biology and algorithm development
    NIH R35GM119850Jul 15, 2016 - Jun 30, 2026
    Role: Principal Investigator

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    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Glycoengineered recombinant alpha1-antitrypsin results in comparable in vitro and in vivo activities to human plasma-derived protein. bioRxiv. 2024 Mar 30. Rocamora F, Schoffelen S, Arnsdorf J, Toth EA, Abdul Y, Cleveland TE, Bjørn SP, Wu MYM, McElvaney NG, Voldborg BGR, Fuerst TR, Lewis NE. PMID: 38585818; PMCID: PMC10996670.
      View in: PubMed   Mentions:
    2. LeGenD: determining N-glycoprofiles using an explainable AI-leveraged model with lectin profiling. bioRxiv. 2024 Mar 30. Li H, Peralta AG, Schoffelen S, Hansen AH, Arnsdorf J, Schinn SM, Skidmore J, Choudhury B, Paulchakrabarti M, Voldborg BG, Chiang AWT, Lewis NE. PMID: 38585977; PMCID: PMC10996628.
      View in: PubMed   Mentions:
    3. Driving towards digital biomanufacturing by CHO genome-scale models. Trends Biotechnol. 2024 Mar 27. Park SY, Choi DH, Song J, Lakshmanan M, Richelle A, Yoon S, Kontoravdi C, Lewis NE, Lee DY. PMID: 38548556.
      View in: PubMed   Mentions:    Fields:    
    4. A Boltzmann model predicts glycan structures from lectin binding. bioRxiv. 2024 Mar 12. Yom A, Chiang A, Lewis NE. PMID: 37333412; PMCID: PMC10274649.
      View in: PubMed   Mentions:
    5. Mechanotransduction-induced interplay between phospholamban and yes-activated protein induces smooth muscle cell hypertrophy. Mucosal Immunol. 2024 Feb 27. Rawson R, Duong L, Tkachenko E, Chiang AWT, Okamoto K, Dohil R, Lewis NE, Kurten R, Abud EM, Aceves SS. PMID: 38423390.
      View in: PubMed   Mentions:    Fields:    
    6. COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling. Metab Eng. 2024 Mar; 82:183-192. Gopalakrishnan S, Johnson W, Valderrama-Gomez MA, Icten E, Tat J, Ingram M, Fung Shek C, Chan PK, Schlegel F, Rolandi P, Kontoravdi C, Lewis NE. PMID: 38387677.
      View in: PubMed   Mentions:    Fields:    
    7. LipidSIM: Inferring mechanistic lipid biosynthesis perturbations from lipidomics with a flexible, low-parameter, Markov modeling framework. Metab Eng. 2024 Mar; 82:110-122. Liang C, Murray S, Li Y, Lee R, Low A, Sasaki S, Chiang AWT, Lin WJ, Mathews J, Barnes W, Lewis NE. PMID: 38311182.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    8. Eosinophilic esophagitis: Shifting immune complexity beyond the eosinophil. J Allergy Clin Immunol. 2024 Mar; 153(3):669-671. Lewis NE, Aceves SS. PMID: 38262501.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    9. The diversification of methods for studying cell-cell interactions and communication. Nat Rev Genet. 2024 Jan 18. Armingol E, Baghdassarian HM, Lewis NE. PMID: 38238518.
      View in: PubMed   Mentions:    Fields:    
    10. Resource allocation in mammalian systems. Biotechnol Adv. 2024 Mar-Apr; 71:108305. Baghdassarian HM, Lewis NE. PMID: 38215956.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    11. Inferring secretory and metabolic pathway activity from omic data with secCellFie. Metab Eng. 2024 Jan; 81:273-285. Masson HO, Samoudi M, Robinson CM, Kuo CC, Weiss L, Shams Ud Doha K, Campos A, Tejwani V, Dahodwala H, Menard P, Voldborg BG, Robasky B, Sharfstein ST, Lewis NE. PMID: 38145748.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    12. Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment. Curr Opin Biotechnol. 2024 Feb; 85:103048. Pong A, Mah CK, Yeo GW, Lewis NE. PMID: 38142648.
      View in: PubMed   Mentions: 1     Fields:    
    13. Predicting pathways for old and new metabolites through clustering. J Theor Biol. 2024 02 07; 578:111684. Siddharth T, Lewis NE. PMID: 38048983.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    14. Hyperon Polarization along the Beam Direction Relative to the Second and Third Harmonic Event Planes in Isobar Collisions at sqrt[s_{NN}]=200  GeV. Phys Rev Lett. 2023 Nov 17; 131(20):202301. Abdulhamid MI, Aboona BE, Adam J, Adams JR, Agakishiev G, Aggarwal I, Aggarwal MM, Ahammed Z, Aitbaev A, Alekseev I, Anderson DM, Aparin A, Aslam S, Atchison J, Averichev GS, Bairathi V, Baker W, Cap JGB, Barish K, Bhagat P, Bhasin A, Bhatta S, Bordyuzhin IG, Brandenburg JD, Brandin AV, Cai XZ, Caines H, Sánchez MCB, Cebra D, Ceska J, Chakaberia I, Chan BK, Chang Z, Chatterjee A, Chen D, Chen J, Chen JH, Chen Z, Cheng J, Cheng Y, Choudhury S, Christie W, Chu X, Crawford HJ, Dale-Gau G, Das A, Daugherity M, Dedovich TG, Deppner IM, Derevschikov AA, Dhamija A, Di Carlo L, Dixit P, Dong X, Drachenberg JL, Duckworth E, Dunlop JC, Engelage J, Eppley G, Esumi S, Evdokimov O, Ewigleben A, Eyser O, Fatemi R, Fazio S, Feng CJ, Feng Y, Finch E, Fisyak Y, Flor FA, Fu C, Gao T, Geurts F, Ghimire N, Gibson A, Gopal K, Gou X, Grosnick D, Gupta A, Hamed A, Han Y, Harasty MD, Harris JW, Harrison-Smith H, He W, He XH, He Y, Hu C, Hu Q, Hu Y, Huang H, Huang HZ, Huang SL, Huang T, Huang X, Huang Y, Huang Y, Humanic TJ, Isenhower D, Isshiki M, Jacobs WW, Jalotra A, Jena C, Ji Y, Jia J, Jin C, Ju X, Judd EG, Kabana S, Kabir ML, Kalinkin D, Kang K, Kapukchyan D, Kauder K, Keane D, Kechechyan A, Kelsey M, Kimelman B, Kiselev A, Knospe AG, Ko HS, Kochenda L, Korobitsin AA, Kravtsov P, Kumar L, Kumar S, Elayavalli RK, Lacey R, Landgraf JM, Lebedev A, Lednicky R, Lee JH, Leung YH, Lewis N, Li C, Li W, Li X, Li Y, Li Y, Li Z, Liang X, Liang Y, Lin T, Liu C, Liu F, Liu G, Liu H, Liu H, Liu L, Liu T, Liu X, Liu Y, Liu Z, Ljubicic T, Llope WJ, Lomicky O, Longacre RS, Loyd EM, Lu T, Lukow NS, Luo XF, Luong VB, Ma L, Ma R, Ma YG, Magdy N, Mallick D, Margetis S, Matis HS, Mazer JA, McNamara G, Mi K, Minaev NG, Mohanty B, Mondal MM, Mooney I, Morozov DA, Mudrokh A, Nagy MI, Nain AS, Nam JD, Nasim M, Neff D, Nelson JM, Nemes DB, Nie M, Nigmatkulov G, Niida T, Nishitani R, Nogach LV, Nonaka T, Odyniec G, Ogawa A, Oh S, Okorokov VA, Okubo K, Page BS, Pak R, Pan J, Pandav A, Pandey AK, Panebratsev Y, Pani T, Parfenov P, Paul A, Perkins C, Pokhrel BR, Posik M, Protzman T, Pruthi NK, Putschke J, Qin Z, Qiu H, Quintero A, Racz C, Radhakrishnan SK, Raha N, Ray RL, Ritter HG, Robertson CW, Rogachevsky OV, Aguilar MAR, Roy D, Ruan L, Sahoo AK, Sahoo NR, Sako H, Salur S, Samigullin E, Sato S, Schmidke WB, Schmitz N, Seger J, Seto R, Seyboth P, Shah N, Shahaliev E, Shanmuganathan PV, Shao T, Sharma M, Sharma N, Sharma R, Sharma SR, Sheikh AI, Shen D, Shen DY, Shen K, Shi SS, Shi Y, Shou QY, Si F, Singh J, Singha S, Sinha P, Skoby MJ, Söhngen Y, Song Y, Srivastava B, Stanislaus TDS, Stewart DJ, Strikhanov M, Stringfellow B, Su Y, Sun C, Sun X, Sun Y, Sun Y, Surrow B, Svirida DN, Sweger ZW, Tamis A, Tang AH, Tang Z, Taranenko A, Tarnowsky T, Thomas JH, Tlusty D, Todoroki T, Tokarev MV, Tomkiel CA, Trentalange S, Tribble RE, Tribedy P, Tsai OD, Tsang CY, Tu Z, Tyler J, Ullrich T, Underwood DG, Upsal I, Van Buren G, Vasiliev AN, Verkest V, Videbæk F, Vokal S, Voloshin SA, Wang F, Wang G, Wang JS, Wang J, Wang X, Wang Y, Wang Y, Wang Y, Wang Z, Webb JC, Weidenkaff PC, Westfall GD, Wieman H, Wilks G, Wissink SW, Wu J, Wu J, Wu X, Wu X, Wu Y, Xi B, Xiao ZG, Xie G, Xie W, Xu H, Xu N, Xu QH, Xu Y, Xu Y, Xu Z, Xu Z, Yan G, Yan Z, Yang C, Yang Q, Yang S, Yang Y, Ye Z, Ye Z, Yi L, Yip K, Yu Y, Zha W, Zhang C, Zhang D, Zhang J, Zhang S, Zhang W, Zhang X, Zhang Y, Zhang Y, Zhang Y, Zhang Y, Zhang ZJ, Zhang Z, Zhang Z, Zhao F, Zhao J, Zhao M, Zhou C, Zhou J, Zhou S, Zhou Y, Zhu X, Zurek M, Zyzak M, STAR Collaboration. PMID: 38039468.
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    15. Pathogen-driven degradation of endogenous and therapeutic antibodies during streptococcal infections. Nat Commun. 2023 10 23; 14(1):6693. Toledo AG, Bratanis E, Velásquez E, Chowdhury S, Olofsson B, Sorrentino JT, Karlsson C, Lewis NE, Esko JD, Collin M, Shannon O, Malmström J. PMID: 37872209; PMCID: PMC10593946.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    16. Identification of hyperosmotic stress-responsive genes in Chinese hamster ovary cells via genome-wide virus-free CRISPR/Cas9 screening. Metab Eng. 2023 Nov; 80:66-77. Kim SH, Shin S, Baek M, Xiong K, Karottki KJC, Hefzi H, Grav LM, Pedersen LE, Kildegaard HF, Lewis NE, Lee JS, Lee GM. PMID: 37709005.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    17. Mitigating biomass composition uncertainties in flux balance analysis using ensemble representations. Comput Struct Biotechnol J. 2023; 21:3736-3745. Choi YM, Choi DH, Lee YQ, Koduru L, Lewis NE, Lakshmanan M, Lee DY. PMID: 37547082; PMCID: PMC10400880.
      View in: PubMed   Mentions: 3  
    18. Spatial Dynamic Subspaces Encode Sex-Specific Schizophrenia Disruptions in Transient Network Overlap and its Links to Genetic Risk. bioRxiv. 2023 Jul 19. Iraji A, Chen J, Lewis N, Faghiri A, Fu Z, Agcaoglu O, Kochunov P, Adhikari BM, Mathalon DH, Pearlson GD, Macciardi F, Preda A, van Erp TGM, Bustillo JR, Díaz-Caneja CM, Andrés-Camazón P, Dhamala M, Adali T, Calhoun VD. PMID: 37503085; PMCID: PMC10370141.
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    19. Whole-body gene expression atlas of an adult metazoan. Sci Adv. 2023 06 23; 9(25):eadg0506. Ghaddar A, Armingol E, Huynh C, Gevirtzman L, Lewis NE, Waterston R, O'Rourke EJ. PMID: 37352352; PMCID: PMC10289653.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    20. Glycosylation shapes the efficacy and safety of diverse protein, gene and cell therapies. Biotechnol Adv. 2023 10; 67:108206. Rocamora F, Peralta AG, Shin S, Sorrentino J, Wu MYM, Toth EA, Fuerst TR, Lewis NE. PMID: 37354999.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    21. Single-cell A/B testing for cell-cell communication. Cell Syst. 2023 06 21; 14(6):428-429. Aamodt CM, Lewis NE. PMID: 37348460.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    22. Measurements of the Elliptic and Triangular Azimuthal Anisotropies in Central ^{3}He+Au, d+Au and p+Au Collisions at sqrt[s_{NN}]=200  GeV. Phys Rev Lett. 2023 Jun 16; 130(24):242301. Abdulhamid MI, Aboona BE, Adam J, Adams JR, Agakishiev G, Aggarwal I, Aggarwal MM, Ahammed Z, Aitbaev A, Alekseev I, Anderson DM, Aparin A, Aslam S, Atchison J, Averichev GS, Bairathi V, Baker W, Ball Cap JG, Barish K, Bhagat P, Bhasin A, Bhatta S, Bordyuzhin IG, Brandenburg JD, Brandin AV, Cai XZ, Caines H, Calderón de la Barca Sánchez M, Cebra D, Ceska J, Chakaberia I, Chan BK, Chang Z, Chatterjee A, Chen D, Chen J, Chen JH, Chen Z, Cheng J, Cheng Y, Choudhury S, Christie W, Chu X, Crawford HJ, Dale-Gau G, Das A, Daugherity M, Dedovich TG, Deppner IM, Derevschikov AA, Dhamija A, Di Carlo L, Didenko L, Dixit P, Dong X, Drachenberg JL, Duckworth E, Dunlop JC, Engelage J, Eppley G, Esumi S, Evdokimov O, Ewigleben A, Eyser O, Fatemi R, Fazio S, Feng CJ, Feng Y, Finch E, Fisyak Y, Flor FA, Fu C, Geurts F, Ghimire N, Gibson A, Gopal K, Gou X, Grosnick D, Gupta A, Hamed A, Han Y, Harasty MD, Harris JW, Harrison-Smith H, He W, He XH, He Y, Hu C, Hu Q, Hu Y, Huang H, Huang HZ, Huang SL, Huang T, Huang X, Huang Y, Huang Y, Humanic TJ, Isenhower D, Isshiki M, Jacobs WW, Jalotra A, Jena C, Ji Y, Jia J, Jin C, Ju X, Judd EG, Kabana S, Kabir ML, Kalinkin D, Kang K, Kapukchyan D, Kauder K, Ke HW, Keane D, Kechechyan A, Kelsey M, Kimelman B, Kiselev A, Knospe AG, Ko HS, Kochenda L, Korobitsin AA, Kravtsov P, Kumar L, Kumar S, Kunnawalkam Elayavalli R, Lacey R, Landgraf JM, Lebedev A, Lednicky R, Lee JH, Leung YH, Lewis N, Li C, Li W, Li X, Li Y, Li Y, Li Z, Liang X, Liang Y, Lin T, Liu C, Liu F, Liu G, Liu H, Liu H, Liu L, Liu T, Liu X, Liu Y, Liu Z, Ljubicic T, Llope WJ, Lomicky O, Longacre RS, Loyd EM, Lu T, Lukow NS, Luo XF, Luong VB, Ma L, Ma R, Ma YG, Magdy N, Mallick D, Margetis S, Matis HS, Mazer JA, McNamara G, Mi K, Minaev NG, Mohanty B, Mondal MM, Mooney I, Morozov DA, Mudrokh A, Nagy MI, Nain AS, Nam JD, Nasim M, Neff D, Nelson JM, Nemes DB, Nie M, Nigmatkulov G, Niida T, Nishitani R, Nogach LV, Nonaka T, Odyniec G, Ogawa A, Oh S, Okorokov VA, Okubo K, Page BS, Pak R, Pan J, Pandav A, Pandey AK, Panebratsev Y, Pani T, Parfenov P, Paul A, Perkins C, Pokhrel BR, Posik M, Protzman T, Pruthi NK, Putschke J, Qin Z, Qiu H, Quintero A, Racz C, Radhakrishnan SK, Raha N, Ray RL, Ritter HG, Robertson CW, Rogachevsky OV, Rosales Aguilar MA, Roy D, Ruan L, Sahoo AK, Sahoo NR, Sako H, Salur S, Samigullin E, Sato S, Schmidke WB, Schmitz N, Seger J, Seto R, Seyboth P, Shah N, Shahaliev E, Shanmuganathan PV, Shao T, Sharma M, Sharma N, Sharma R, Sharma SR, Sheikh AI, Shen DY, Shen K, Shi SS, Shi Y, Shou QY, Si F, Singh J, Singha S, Sinha P, Skoby MJ, Söhngen Y, Song Y, Srivastava B, Stanislaus TDS, Stewart DJ, Strikhanov M, Stringfellow B, Su Y, Sun C, Sun X, Sun Y, Sun Y, Surrow B, Svirida DN, Sweger ZW, Tamis A, Tang AH, Tang Z, Taranenko A, Tarnowsky T, Thomas JH, Tlusty D, Todoroki T, Tokarev MV, Tomkiel CA, Trentalange S, Tribble RE, Tribedy P, Tsai OD, Tsang CY, Tu Z, Ullrich T, Underwood DG, Upsal I, Van Buren G, Vasiliev AN, Verkest V, Videbæk F, Vokal S, Voloshin SA, Wang F, Wang G, Wang JS, Wang X, Wang Y, Wang Y, Wang Y, Wang Z, Webb JC, Weidenkaff PC, Westfall GD, Wieman H, Wilks G, Wissink SW, Wu J, Wu J, Wu X, Wu Y, Xi B, Xiao ZG, Xie G, Xie W, Xu H, Xu N, Xu QH, Xu Y, Xu Y, Xu Z, Xu Z, Yan G, Yan Z, Yang C, Yang Q, Yang S, Yang Y, Ye Z, Ye Z, Yi L, Yip K, Yu Y, Zha W, Zhang C, Zhang D, Zhang J, Zhang S, Zhang W, Zhang X, Zhang Y, Zhang Y, Zhang Y, Zhang ZJ, Zhang Z, Zhang Z, Zhao F, Zhao J, Zhao M, Zhou C, Zhou J, Zhou S, Zhou Y, Zhu X, Zurek M, Zyzak M, STAR Collaboration. PMID: 37390421.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    23. Variant STAT4 and Response to Ruxolitinib in an Autoinflammatory Syndrome. N Engl J Med. 2023 Jun 15; 388(24):2241-2252. Baghdassarian H, Blackstone SA, Clay OS, Philips R, Matthiasardottir B, Nehrebecky M, Hua VK, McVicar R, Liu Y, Tucker SM, Randazzo D, Deuitch N, Rosenzweig S, Mark A, Sasik R, Fisch KM, Pimpale Chavan P, Eren E, Watts NR, Ma CA, Gadina M, Schwartz DM, Sanyal A, Werner G, Murdock DR, Horita N, Chowdhury S, Dimmock D, Jepsen K, Remmers EF, Goldbach-Mansky R, Gahl WA, O'Shea JJ, Milner JD, Lewis NE, Chang J, Kastner DL, Torok K, Oda H, Putnam CD, Broderick L. PMID: 37256972; PMCID: PMC10392571.
      View in: PubMed   Mentions: 7     Fields:    
    24. Observation of Directed Flow of Hypernuclei _{Λ}^{3}H and _{Λ}^{4}H in sqrt[s_{NN}]=3  GeV Au+Au Collisions at RHIC. Phys Rev Lett. 2023 May 26; 130(21):212301. Aboona BE, Adam J, Adams JR, Agakishiev G, Aggarwal I, Aggarwal MM, Ahammed Z, Aitbaev A, Alekseev I, Anderson DM, Aparin A, Atchison J, Averichev GS, Bairathi V, Baker W, Ball Cap JG, Barish K, Bhagat P, Bhasin A, Bhatta S, Bordyuzhin IG, Brandenburg JD, Brandin AV, Cai XZ, Caines H, Calderón de la Barca Sánchez M, Cebra D, Ceska J, Chakaberia I, Chan BK, Chang Z, Chen D, Chen J, Chen JH, Chen Z, Cheng J, Cheng Y, Choudhury S, Christie W, Chu X, Crawford HJ, Dale-Gau G, Das A, Daugherity M, Dedovich TG, Deppner IM, Derevschikov AA, Dhamija A, Di Carlo L, Didenko L, Dixit P, Dong X, Drachenberg JL, Duckworth E, Dunlop JC, Engelage J, Eppley G, Esumi S, Evdokimov O, Ewigleben A, Eyser O, Fatemi R, Fazio S, Feng CJ, Feng Y, Finch E, Fisyak Y, Flor FA, Fu C, Geurts F, Ghimire N, Gibson A, Gopal K, Gou X, Grosnick D, Gupta A, Hamed A, Han Y, Harasty MD, Harris JW, Harrison H, He W, He XH, He Y, Hu C, Hu Q, Hu Y, Huang H, Huang HZ, Huang SL, Huang T, Huang X, Huang Y, Huang Y, Humanic TJ, Isenhower D, Isshiki M, Jacobs WW, Jalotra A, Jena C, Ji Y, Jia J, Jin C, Ju X, Judd EG, Kabana S, Kabir ML, Kalinkin D, Kang K, Kapukchyan D, Kauder K, Ke HW, Keane D, Kechechyan A, Kelsey M, Kimelman B, Kiselev A, Knospe AG, Ko HS, Kochenda L, Korobitsin AA, Kravtsov P, Kumar L, Kumar S, Kunnawalkam Elayavalli R, Lacey R, Landgraf JM, Lebedev A, Lednicky R, Lee JH, Leung YH, Lewis N, Li C, Li C, Li W, Li X, Li Y, Li Y, Li Z, Liang X, Liang Y, Lin T, Liu C, Liu F, Liu H, Liu H, Liu L, Liu T, Liu X, Liu Y, Liu Z, Ljubicic T, Llope WJ, Lomicky O, Longacre RS, Loyd E, Lu T, Lukow NS, Luo XF, Luong VB, Ma L, Ma R, Ma YG, Magdy N, Mallick D, Margetis S, Matis HS, Mazer JA, McNamara G, Mi K, Minaev NG, Mohanty B, Mooney I, Morozov DA, Mudrokh A, Nagy MI, Nain AS, Nam JD, Nasim M, Neff D, Nelson JM, Nemes DB, Nie M, Nigmatkulov G, Niida T, Nishitani R, Nogach LV, Nonaka T, Nunes AS, Odyniec G, Ogawa A, Oh S, Okorokov VA, Okubo K, Page BS, Pak R, Pan J, Pandav A, Pandey AK, Panebratsev Y, Pani T, Parfenov P, Paul A, Perkins C, Pokhrel BR, Posik M, Protzman T, Pruthi NK, Putschke J, Qin Z, Qiu H, Quintero A, Racz C, Radhakrishnan SK, Raha N, Ray RL, Ritter HG, Robertson CW, Rogachevsky OV, Rosales Aguilar MA, Roy D, Ruan L, Sahoo AK, Sahoo NR, Sako H, Salur S, Samigullin E, Sato S, Schmidke WB, Schmitz N, Seger J, Seto R, Seyboth P, Shah N, Shahaliev E, Shanmuganathan PV, Shao M, Shao T, Sharma M, Sharma N, Sharma R, Sharma SR, Sheikh AI, Shen DY, Shen K, Shi SS, Shi Y, Shou QY, Si F, Singh J, Singha S, Sinha P, Skoby MJ, Söhngen Y, Song Y, Srivastava B, Stanislaus TDS, Stewart DJ, Strikhanov M, Stringfellow B, Su Y, Sun C, Sun X, Sun Y, Sun Y, Surrow B, Svirida DN, Sweger ZW, Tamis A, Tang AH, Tang Z, Taranenko A, Tarnowsky T, Thomas JH, Tlusty D, Todoroki T, Tokarev MV, Tomkiel CA, Trentalange S, Tribble RE, Tribedy P, Tsai OD, Tsang CY, Tu Z, Ullrich T, Underwood DG, Upsal I, Van Buren G, Vasiliev AN, Verkest V, Videbæk F, Vokal S, Voloshin SA, Wang F, Wang G, Wang JS, Wang X, Wang Y, Wang Y, Wang Y, Wang Z, Webb JC, Weidenkaff PC, Westfall GD, Wieman H, Wilks G, Wissink SW, Wu J, Wu J, Wu X, Wu Y, Xi B, Xiao ZG, Xie W, Xu H, Xu N, Xu QH, Xu Y, Xu Y, Xu Z, Xu Z, Yan G, Yan Z, Yang C, Yang Q, Yang S, Yang Y, Ye Z, Ye Z, Yi L, Yip K, Yu Y, Zha W, Zhang C, Zhang D, Zhang J, Zhang S, Zhang X, Zhang Y, Zhang Y, Zhang Y, Zhang ZJ, Zhang Z, Zhang Z, Zhao F, Zhao J, Zhao M, Zhou C, Zhou J, Zhou S, Zhou Y, Zhu X, Zurek M, Zyzak M, STAR Collaboration. PMID: 37295104.
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    25. Reconstructing the cell-cell interaction network among mouse immune cells. Biotechnol Bioeng. 2023 09; 120(9):2756-2764. Azadian S, Doustmohammadi A, Naseri M, Khodarahmi M, Arab SS, Yazdanifar M, Zahiri J, Lewis NE. PMID: 37227044; PMCID: PMC10524935.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    26. Beam Energy Dependence of Triton Production and Yield Ratio (N_{t}×N_{p}/N_{d}^{2}) in Au+Au Collisions at RHIC. Phys Rev Lett. 2023 May 19; 130(20):202301. Abdulhamid MI, Aboona BE, Adam J, Adams JR, Agakishiev G, Aggarwal I, Aggarwal MM, Ahammed Z, Aitbaev A, Alekseev I, Anderson DM, Aparin A, Aslam S, Atchison J, Averichev GS, Bairathi V, Baker W, Ball Cap JG, Barish K, Bhagat P, Bhasin A, Bhatta S, Bordyuzhin IG, Brandenburg JD, Brandin AV, Cai XZ, Caines H, Calderón de la Barca Sánchez M, Cebra D, Ceska J, Chakaberia I, Chan BK, Chang Z, Chatterjee A, Chen D, Chen J, Chen JH, Chen Z, Cheng J, Cheng Y, Choudhury S, Christie W, Chu X, Crawford HJ, Dale-Gau G, Das A, Daugherity M, Dedovich TG, Deppner IM, Derevschikov AA, Dhamija A, Di Carlo L, Didenko L, Dixit P, Dong X, Drachenberg JL, Duckworth E, Dunlop JC, Engelage J, Eppley G, Esumi S, Evdokimov O, Ewigleben A, Eyser O, Fatemi R, Fazio S, Feng CJ, Feng Y, Finch E, Fisyak Y, Flor FA, Fu C, Geurts F, Ghimire N, Gibson A, Gopal K, Gou X, Grosnick D, Gupta A, Hamed A, Han Y, Harasty MD, Harris JW, Harrison-Smith H, He W, He XH, He Y, Hu C, Hu Q, Hu Y, Huang H, Huang HZ, Huang SL, Huang T, Huang X, Huang Y, Huang Y, Humanic TJ, Isenhower D, Isshiki M, Jacobs WW, Jalotra A, Jena C, Ji Y, Jia J, Jin C, Ju X, Judd EG, Kabana S, Kabir ML, Kalinkin D, Kang K, Kapukchyan D, Kauder K, Ke HW, Keane D, Kechechyan A, Kelsey M, Kimelman B, Kiselev A, Knospe AG, Ko HS, Kochenda L, Korobitsin AA, Kravtsov P, Kumar L, Kumar S, Kunnawalkam Elayavalli R, Lacey R, Landgraf JM, Lebedev A, Lednicky R, Lee JH, Leung YH, Lewis N, Li C, Li W, Li X, Li Y, Li Y, Li Z, Liang X, Liang Y, Lin T, Liu C, Liu F, Liu H, Liu H, Liu L, Liu T, Liu X, Liu Y, Liu Z, Ljubicic T, Llope WJ, Lomicky O, Longacre RS, Loyd EM, Lu T, Lukow NS, Luo XF, Luong VB, Ma L, Ma R, Ma YG, Magdy N, Mallick D, Margetis S, Matis HS, Mazer JA, McNamara G, Mi K, Minaev NG, Mohanty B, Mondal MM, Mooney I, Morozov DA, Mudrokh A, Nagy MI, Nain AS, Nam JD, Nasim M, Neff D, Nelson JM, Nemes DB, Nie M, Nigmatkulov G, Niida T, Nishitani R, Nogach LV, Nonaka T, Odyniec G, Ogawa A, Oh S, Okorokov VA, Okubo K, Page BS, Pak R, Pan J, Pandav A, Pandey AK, Panebratsev Y, Pani T, Parfenov P, Paul A, Perkins C, Pokhrel BR, Posik M, Protzman T, Pruthi NK, Putschke J, Qin Z, Qiu H, Quintero A, Racz C, Radhakrishnan SK, Raha N, Ray RL, Ritter HG, Robertson CW, Rogachevsky OV, Rosales Aguilar MA, Roy D, Ruan L, Sahoo AK, Sahoo NR, Sako H, Salur S, Samigullin E, Sato S, Schmidke WB, Schmitz N, Seger J, Seto R, Seyboth P, Shah N, Shahaliev E, Shanmuganathan PV, Shao T, Sharma M, Sharma N, Sharma R, Sharma SR, Sheikh AI, Shen DY, Shen K, Shi SS, Shi Y, Shou QY, Si F, Singh J, Singha S, Sinha P, Skoby MJ, Söhngen Y, Song Y, Srivastava B, Stanislaus TDS, Stewart DJ, Strikhanov M, Stringfellow B, Su Y, Sun C, Sun X, Sun Y, Sun Y, Surrow B, Svirida DN, Sweger ZW, Tamis A, Tang AH, Tang Z, Taranenko A, Tarnowsky T, Thomas JH, Tlusty D, Todoroki T, Tokarev MV, Tomkiel CA, Trentalange S, Tribble RE, Tribedy P, Tsai OD, Tsang CY, Tu Z, Ullrich T, Underwood DG, Upsal I, Van Buren G, Vasiliev AN, Verkest V, Videbæk F, Vokal S, Voloshin SA, Wang F, Wang G, Wang JS, Wang X, Wang Y, Wang Y, Wang Y, Wang Z, Webb JC, Weidenkaff PC, Westfall GD, Wieman H, Wilks G, Wissink SW, Wu J, Wu J, Wu X, Wu Y, Xi B, Xiao ZG, Xie G, Xie W, Xu H, Xu N, Xu QH, Xu Y, Xu Y, Xu Z, Xu Z, Yan G, Yan Z, Yang C, Yang Q, Yang S, Yang Y, Ye Z, Ye Z, Yi L, Yip K, Yu N, Yu Y, Zha W, Zhang C, Zhang D, Zhang J, Zhang S, Zhang X, Zhang Y, Zhang Y, Zhang Y, Zhang ZJ, Zhang Z, Zhang Z, Zhao F, Zhao J, Zhao M, Zhou C, Zhou J, Zhou S, Zhou Y, Zhu X, Zurek M, Zyzak M, STAR Collaboration. PMID: 37267557.
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    27. Inferring secretory and metabolic pathway activity from omic data with secCellFie. bioRxiv. 2023 May 07. Masson HO, Samoudi M, Robinson CM, Kuo CC, Weiss L, Doha KSU, Campos A, Tejwani V, Dahodwala H, Menard P, Voldborg BG, Sharfstein ST, Lewis NE. PMID: 37205389; PMCID: PMC10187314.
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    28. Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples. bioRxiv. 2023 Apr 30. Baghdassarian H, Dimitrov D, Armingol E, Saez-Rodriguez J, Lewis NE. PMID: 37162916; PMCID: PMC10168343.
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    29. GlycoMME, a Markov modeling platform for studying N-glycosylation biosynthesis from glycomics data. STAR Protoc. 2023 Apr 21; 4(2):102244. Liang C, Chiang AWT, Lewis NE. PMID: 37086409; PMCID: PMC10160804.
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    30. From observational to actionable: rethinking omics in biologics production. Trends Biotechnol. 2023 09; 41(9):1127-1138. Masson HO, Karottki KJC, Tat J, Hefzi H, Lewis NE. PMID: 37062598; PMCID: PMC10524802.
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    31. Measurement of Sequential ϒ Suppression in Au+Au Collisions at sqrt[s_{NN}]=200  GeV with the STAR Experiment. Phys Rev Lett. 2023 Mar 17; 130(11):112301. Aboona BE, Adam J, Adamczyk L, Adams JR, Aggarwal I, Aggarwal MM, Ahammed Z, Anderson DM, Aschenauer EC, Atchison J, Bairathi V, Baker W, Ball Cap JG, Barish K, Bellwied R, Bhagat P, Bhasin A, Bhatta S, Bielcik J, Bielcikova J, Brandenburg JD, Cai XZ, Caines H, Calderón de la Barca Sánchez M, Cebra D, Ceska J, Chakaberia I, Chaloupka P, Chan BK, Chang Z, Chen D, Chen J, Chen JH, Chen Z, Cheng J, Cheng Y, Choudhury S, Christie W, Chu X, Crawford HJ, Csanád M, Dale-Gau G, Das A, Daugherity M, Deppner IM, Dhamija A, Di Carlo L, Didenko L, Dixit P, Dong X, Drachenberg JL, Duckworth E, Dunlop JC, Engelage J, Eppley G, Esumi S, Evdokimov O, Ewigleben A, Eyser O, Fatemi R, Fazio S, Feng CJ, Feng Y, Finch E, Fisyak Y, Flor FA, Fu C, Gagliardi CA, Galatyuk T, Geurts F, Ghimire N, Gibson A, Gopal K, Gou X, Grosnick D, Gupta A, Guryn W, Hamed A, Han Y, Harabasz S, Harasty MD, Harris JW, Harrison H, He W, He XH, He Y, Heppelmann S, Herrmann N, Holub L, Hu C, Hu Q, Hu Y, Huang H, Huang HZ, Huang SL, Huang T, Huang X, Huang Y, Huang Y, Humanic TJ, Isenhower D, Isshiki M, Jacobs WW, Jalotra A, Jena C, Jentsch A, Ji Y, Jia J, Jin C, Ju X, Judd EG, Kabana S, Kabir ML, Kagamaster S, Kalinkin D, Kang K, Kapukchyan D, Kauder K, Ke HW, Keane D, Kelsey M, Khyzhniak YV, Kikola DP, Kimelman B, Kincses D, Kisel I, Kiselev A, Knospe AG, Ko HS, Kosarzewski LK, Kramarik L, Kumar L, Kumar S, Kunnawalkam Elayavalli R, Lacey R, Landgraf JM, Lauret J, Lebedev A, Lee JH, Leung YH, Lewis N, Li C, Li C, Li W, Li X, Li Y, Li Y, Li Z, Liang X, Liang Y, Licenik R, Lin T, Lisa MA, Liu C, Liu F, Liu H, Liu H, Liu L, Liu T, Liu X, Liu Y, Liu Z, Ljubicic T, Llope WJ, Lomicky O, Longacre RS, Loyd E, Lu T, Lukow NS, Luo XF, Ma L, Ma R, Ma YG, Magdy N, Mallick D, Margetis S, Markert C, Matis HS, Mazer JA, McNamara G, Mi K, Mioduszewski S, Mohanty B, Mooney I, Mukherjee A, Nagy MI, Nain AS, Nam JD, Nasim M, Neff D, Nelson JM, Nemes DB, Nie M, Niida T, Nishitani R, Nonaka T, Nunes AS, Odyniec G, Ogawa A, Oh S, Okubo K, Page BS, Pak R, Pan J, Pandav A, Pandey AK, Pani T, Paul A, Pawlik B, Pawlowska D, Perkins C, Pluta J, Pokhrel BR, Posik M, Protzman T, Prozorova V, Pruthi NK, Przybycien M, Putschke J, Qin Z, Qiu H, Quintero A, Racz C, Radhakrishnan SK, Raha N, Ray RL, Reed R, Ritter HG, Robertson CW, Robotkova M, Romero JL, Rosales Aguilar MA, Roy D, Roy Chowdhury P, Ruan L, Sahoo AK, Sahoo NR, Sako H, Salur S, Sato S, Schmidke WB, Schmitz N, Seck FJ, Seger J, Seto R, Seyboth P, Shah N, Shanmuganathan PV, Shao M, Shao T, Sharma M, Sharma N, Sharma R, Sharma SR, Sheikh AI, Shen DY, Shen K, Shi SS, Shi Y, Shou QY, Si F, Singh J, Singha S, Sinha P, Skoby MJ, Smirnov N, Söhngen Y, Song Y, Srivastava B, Stanislaus TDS, Stefaniak M, Stewart DJ, Stringfellow B, Su Y, Suaide AAP, Sumbera M, Sun C, Sun X, Sun Y, Sun Y, Surrow B, Sweger ZW, Szymanski P, Tamis A, Tang AH, Tang Z, Tarnowsky T, Thomas JH, Timmins AR, Tlusty D, Todoroki T, Tomkiel CA, Trentalange S, Tribble RE, Tribedy P, Truhlar T, Trzeciak BA, Tsai OD, Tsang CY, Tu Z, Ullrich T, Underwood DG, Upsal I, Van Buren G, Vanek J, Vassiliev I, Verkest V, Videbæk F, Voloshin SA, Wang F, Wang G, Wang JS, Wang X, Wang Y, Wang Y, Wang Y, Wang Z, Webb JC, Weidenkaff PC, Westfall GD, Wielanek D, Wieman H, Wilks G, Wissink SW, Witt R, Wu J, Wu J, Wu X, Wu Y, Xi B, Xiao ZG, Xie W, Xu H, Xu N, Xu QH, Xu Y, Xu Y, Xu Z, Xu Z, Yan G, Yan Z, Yang C, Yang Q, Yang S, Yang Y, Ye Z, Ye Z, Yi L, Yip K, Yu Y, Zbroszczyk H, Zha W, Zhang C, Zhang D, Zhang J, Zhang S, Zhang X, Zhang Y, Zhang Y, Zhang Y, Zhang ZJ, Zhang Z, Zhang Z, Zhao F, Zhao J, Zhao M, Zhou C, Zhou J, Zhou S, Zhou Y, Zhu X, Zurek M, Zyzak M, STAR Collaboration. PMID: 37001106.
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    32. Preparing glycomics data for robust statistical analysis with GlyCompareCT. STAR Protoc. 2023 Mar 13; 4(2):102162. Zhang Y, Krishnan S, Bao B, Chiang AWT, Sorrentino JT, Schinn SM, Kellman BP, Lewis NE. PMID: 36920914; PMCID: PMC10025275.
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    33. Beam Energy Dependence of Fifth- and Sixth-Order Net-Proton Number Fluctuations in Au+Au Collisions at RHIC. Phys Rev Lett. 2023 Feb 24; 130(8):082301. Aboona BE, Adam J, Adamczyk L, Adams JR, Aggarwal I, Aggarwal MM, Ahammed Z, Anderson DM, Aschenauer EC, Atchison J, Bairathi V, Baker W, Ball Cap JG, Barish K, Bellwied R, Bhagat P, Bhasin A, Bhatta S, Bielcik J, Bielcikova J, Brandenburg JD, Cai XZ, Caines H, Calderón de la Barca Sánchez M, Cebra D, Ceska J, Chakaberia I, Chaloupka P, Chan BK, Chang Z, Chen D, Chen J, Chen JH, Chen Z, Cheng J, Cheng Y, Choudhury S, Christie W, Chu X, Crawford HJ, Csanád M, Dale-Gau G, Das A, Daugherity M, Deppner IM, Dhamija A, Di Carlo L, Didenko L, Dixit P, Dong X, Drachenberg JL, Duckworth E, Dunlop JC, Engelage J, Eppley G, Esumi S, Evdokimov O, Ewigleben A, Eyser O, Fatemi R, Fazio S, Feng CJ, Feng Y, Finch E, Fisyak Y, Flor FA, Fu C, Gagliardi CA, Galatyuk T, Geurts F, Ghimire N, Gibson A, Gopal K, Gou X, Grosnick D, Gupta A, Guryn W, Hamed A, Han Y, Harabasz S, Harasty MD, Harris JW, Harrison H, He W, He XH, He Y, Heppelmann S, Herrmann N, Holub L, Hu C, Hu Q, Hu Y, Huang H, Huang HZ, Huang SL, Huang T, Huang X, Huang Y, Huang Y, Humanic TJ, Isenhower D, Isshiki M, Jacobs WW, Jalotra A, Jena C, Jentsch A, Ji Y, Jia J, Jin C, Ju X, Judd EG, Kabana S, Kabir ML, Kagamaster S, Kalinkin D, Kang K, Kapukchyan D, Kauder K, Ke HW, Keane D, Kelsey M, Khyzhniak YV, Kikola DP, Kimelman B, Kincses D, Kisel I, Kiselev A, Knospe AG, Ko HS, Kosarzewski LK, Kramarik L, Kumar L, Kumar S, Kunnawalkam Elayavalli R, Lacey R, Landgraf JM, Lauret J, Lebedev A, Lee JH, Leung YH, Lewis N, Li C, Li C, Li W, Li X, Li Y, Li Y, Li Z, Liang X, Liang Y, Licenik R, Lin T, Lisa MA, Liu C, Liu F, Liu H, Liu H, Liu L, Liu T, Liu X, Liu Y, Liu Z, Ljubicic T, Llope WJ, Lomicky O, Longacre RS, Loyd E, Lu T, Lukow NS, Luo XF, Ma L, Ma R, Ma YG, Magdy N, Mallick D, Margetis S, Markert C, Matis HS, Mazer JA, McNamara G, Mi K, Mioduszewski S, Mohanty B, Mooney I, Mukherjee A, Nagy MI, Nain AS, Nam JD, Nasim M, Neff D, Nelson JM, Nemes DB, Nie M, Niida T, Nishitani R, Nonaka T, Nunes AS, Odyniec G, Ogawa A, Oh S, Okubo K, Page BS, Pak R, Pan J, Pandav A, Pandey AK, Pani T, Paul A, Pawlik B, Pawlowska D, Perkins C, Pluta J, Pokhrel BR, Posik M, Protzman T, Prozorova V, Pruthi NK, Przybycien M, Putschke J, Qin Z, Qiu H, Quintero A, Racz C, Radhakrishnan SK, Raha N, Ray RL, Reed R, Ritter HG, Robertson CW, Robotkova M, Romero JL, Rosales Aguilar MA, Roy D, Roy Chowdhury P, Ruan L, Sahoo AK, Sahoo NR, Sako H, Salur S, Sato S, Schmidke WB, Schmitz N, Seck FJ, Seger J, Seto R, Seyboth P, Shah N, Shanmuganathan PV, Shao M, Shao T, Sharma M, Sharma N, Sharma R, Sharma SR, Sheikh AI, Shen DY, Shen K, Shi SS, Shi Y, Shou QY, Si F, Singh J, Singha S, Sinha P, Skoby MJ, Smirnov N, Söhngen Y, Song Y, Srivastava B, Stanislaus TDS, Stefaniak M, Stewart DJ, Stringfellow B, Su Y, Suaide AAP, Sumbera M, Sun C, Sun X, Sun Y, Sun Y, Surrow B, Sweger ZW, Szymanski P, Tamis A, Tang AH, Tang Z, Tarnowsky T, Thomas JH, Timmins AR, Tlusty D, Todoroki T, Tomkiel CA, Trentalange S, Tribble RE, Tribedy P, Truhlar T, Trzeciak BA, Tsai OD, Tsang CY, Tu Z, Ullrich T, Underwood DG, Upsal I, Van Buren G, Vanek J, Vassiliev I, Verkest V, Videbæk F, Voloshin SA, Wang F, Wang G, Wang JS, Wang X, Wang Y, Wang Y, Wang Y, Wang Z, Webb JC, Weidenkaff PC, Westfall GD, Wielanek D, Wieman H, Wilks G, Wissink SW, Witt R, Wu J, Wu J, Wu X, Wu Y, Xi B, Xiao ZG, Xie W, Xu H, Xu N, Xu QH, Xu Y, Xu Y, Xu Z, Xu Z, Yan G, Yan Z, Yang C, Yang Q, Yang S, Yang Y, Ye Z, Ye Z, Yi L, Yip K, Yu Y, Zbroszczyk H, Zha W, Zhang C, Zhang D, Zhang J, Zhang S, Zhang X, Zhang Y, Zhang Y, Zhang Y, Zhang ZJ, Zhang Z, Zhang Z, Zhao F, Zhao J, Zhao M, Zhou C, Zhou J, Zhou S, Zhou Y, Zhu X, Zurek M, Zyzak M, STAR Collaboration. PMID: 36898098.
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    34. ImmCellFie: A user-friendly web-based platform to infer metabolic function from omics data. STAR Protoc. 2023 03 17; 4(1):102069. Masson HO, Borland D, Reilly J, Telleria A, Shrivastava S, Watson M, Bustillos L, Li Z, Capps L, Kellman BP, King ZA, Richelle A, Lewis NE, Robasky K. PMID: 36853701; PMCID: PMC9898792.
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    35. CHOGlycoNET: Comprehensive glycosylation reaction network for CHO cells. Metab Eng. 2023 03; 76:87-96. Kotidis P, Donini R, Arnsdorf J, Hansen AH, Voldborg BGR, Chiang AWT, Haslam SM, Betenbaugh M, Jimenez Del Val I, Lewis NE, Krambeck F, Kontoravdi C. PMID: 36610518.
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    36. Enhancing CHO cell productivity through a dual selection system using Aspg and Gs in glutamine free medium. Biotechnol Bioeng. 2023 04; 120(4):1159-1166. Ha TK, Òdena A, Karottki KJC, Kim CL, Hefzi H, Lee GM, Faustrup Kildegaard H, Nielsen LK, Grav LM, Lewis NE. PMID: 36562657.
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    37. Guidelines for extracting biologically relevant context-specific metabolic models using gene expression data. Metab Eng. 2023 01; 75:181-191. Gopalakrishnan S, Joshi CJ, Valderrama-Gómez MÁ, Icten E, Rolandi P, Johnson W, Kontoravdi C, Lewis NE. PMID: 36566974; PMCID: PMC10258867.
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    38. An improved algorithm for flux variability analysis. BMC Bioinformatics. 2022 Dec 19; 23(1):550. Kenefake D, Armingol E, Lewis NE, Pistikopoulos EN. PMID: 36536290; PMCID: PMC9761963.
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    39. Simple and practical sialoglycan encoding system reveals vast diversity in nature and identifies a universal sialoglycan-recognizing probe derived from AB5 toxin B subunits. Glycobiology. 2022 11 22; 32(12):1101-1115. Sasmal A, Khan N, Khedri Z, Kellman BP, Srivastava S, Verhagen A, Yu H, Bruntse AB, Diaz S, Varki N, Beddoe T, Paton AW, Paton JC, Chen X, Lewis NE, Varki A. PMID: 36048714; PMCID: PMC9680115.
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    40. Inferring a spatial code of cell-cell interactions across a whole animal body. PLoS Comput Biol. 2022 11; 18(11):e1010715. Armingol E, Ghaddar A, Joshi CJ, Baghdassarian H, Shamie I, Chan J, Her HL, Berhanu S, Dar A, Rodriguez-Armstrong F, Yang O, O'Rourke EJ, Lewis NE. PMID: 36395331; PMCID: PMC9714814.
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    41. A predictive ensemble classifier for the gene expression diagnosis of ASD at ages 1 to 4 years. Mol Psychiatry. 2023 02; 28(2):822-833. Bao B, Zahiri J, Gazestani VH, Lopez L, Xiao Y, Kim R, Wen TH, Chiang AWT, Nalabolu S, Pierce K, Robasky K, Wang T, Hoekzema K, Eichler EE, Lewis NE, Courchesne E. PMID: 36266569; PMCID: PMC9908553.
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    42. Evidence for Nonlinear Gluon Effects in QCD and Their Mass Number Dependence at STAR. Phys Rev Lett. 2022 Aug 26; 129(9):092501. Abdallah MS, Aboona BE, Adam J, Adamczyk L, Adams JR, Adkins JK, Agakishiev G, Aggarwal I, Aggarwal MM, Ahammed Z, Alekseev I, Anderson DM, Aparin A, Aschenauer EC, Ashraf MU, Atetalla FG, Attri A, Averichev GS, Bairathi V, Baker W, Ball Cap JG, Barish K, Behera A, Bellwied R, Bhagat P, Bhasin A, Bielcik J, Bielcikova J, Bordyuzhin IG, Brandenburg JD, Brandin AV, Bunzarov I, Cai XZ, Caines H, Calderón de la Barca Sánchez M, Cebra D, Chakaberia I, Chaloupka P, Chan BK, Chang FH, Chang Z, Chankova-Bunzarova N, Chatterjee A, Chattopadhyay S, Chen D, Chen J, Chen JH, Chen X, Chen Z, Cheng J, Chevalier M, Choudhury S, Christie W, Chu X, Crawford HJ, Csanád M, Daugherity M, Dedovich TG, Deppner IM, Derevschikov AA, Dhamija A, Di Carlo L, Didenko L, Dixit P, Dong X, Drachenberg JL, Duckworth E, Dunlop JC, Elsey N, Engelage J, Eppley G, Esumi S, Evdokimov O, Ewigleben A, Eyser O, Fatemi R, Fawzi FM, Fazio S, Federic P, Fedorisin J, Feng CJ, Feng Y, Filip P, Finch E, Fisyak Y, Francisco A, Fu C, Fulek L, Gagliardi CA, Galatyuk T, Geurts F, Ghimire N, Gibson A, Gopal K, Gou X, Grosnick D, Gupta A, Guryn W, Hamad AI, Hamed A, Han Y, Harabasz S, Harasty MD, Harris JW, Harrison H, He S, He W, He XH, He Y, Heppelmann S, Heppelmann S, Herrmann N, Hoffman E, Holub L, Hu Y, Huang H, Huang HZ, Huang SL, Huang T, Huang X, Huang Y, Humanic TJ, Igo G, Isenhower D, Jacobs WW, Jena C, Jentsch A, Ji Y, Jia J, Jiang K, Ju X, Judd EG, Kabana S, Kabir ML, Kagamaster S, Kalinkin D, Kang K, Kapukchyan D, Kauder K, Ke HW, Keane D, Kechechyan A, Kelsey M, Khyzhniak YV, Kikola DP, Kim C, Kimelman B, Kincses D, Kisel I, Kiselev A, Knospe AG, Ko HS, Kochenda L, Kosarzewski LK, Kramarik L, Kravtsov P, Kumar L, Kumar S, Kunnawalkam Elayavalli R, Kwasizur JH, Lacey R, Lan S, Landgraf JM, Lauret J, Lebedev A, Lednicky R, Lee JH, Leung YH, Lewis N, Li C, Li C, Li W, Li X, Li Y, Liang X, Liang Y, Licenik R, Lin T, Lin Y, Lisa MA, Liu F, Liu H, Liu H, Liu P, Liu T, Liu X, Liu Y, Liu Z, Ljubicic T, Llope WJ, Longacre RS, Loyd E, Lukow NS, Luo XF, Ma L, Ma R, Ma YG, Magdy Abdelwahab Abdelrahman N, Mallick D, Margetis S, Markert C, Matis HS, Mazer JA, Minaev NG, Mioduszewski S, Mohanty B, Mondal MM, Mooney I, Morozov DA, Mukherjee A, Nagy M, Nam JD, Nasim M, Nayak K, Neff D, Nelson JM, Nemes DB, Nie M, Nigmatkulov G, Niida T, Nishitani R, Nogach LV, Nonaka T, Nunes AS, Odyniec G, Ogawa A, Oh S, Okorokov VA, Page BS, Pak R, Pan J, Pandav A, Pandey AK, Panebratsev Y, Parfenov P, Pawlik B, Pawlowska D, Perkins C, Pinsky L, Pintér RL, Pluta J, Pokhrel BR, Ponimatkin G, Porter J, Posik M, Prozorova V, Pruthi NK, Przybycien M, Putschke J, Qiu H, Quintero A, Racz C, Radhakrishnan SK, Raha N, Ray RL, Reed R, Ritter HG, Robotkova M, Rogachevskiy OV, Romero JL, Roy D, Ruan L, Rusnak J, Sahoo AK, Sahoo NR, Sako H, Salur S, Sandweiss J, Sato S, Schmidke WB, Schmitz N, Schweid BR, Seck F, Seger J, Sergeeva M, Seto R, Seyboth P, Shah N, Shahaliev E, Shanmuganathan PV, Shao M, Shao T, Sheikh AI, Shen DY, Shi SS, Shi Y, Shou QY, Sichtermann EP, Sikora R, Simko M, Singh J, Singha S, Skoby MJ, Smirnov N, Söhngen Y, Solyst W, Sorensen P, Spinka HM, Srivastava B, Stanislaus TDS, Stefaniak M, Stewart DJ, Strikhanov M, Stringfellow B, Suaide AAP, Sumbera M, Summa B, Sun XM, Sun X, Sun Y, Sun Y, Surrow B, Svirida DN, Sweger ZW, Szymanski P, Tang AH, Tang Z, Taranenko A, Tarnowsky T, Thomas JH, Timmins AR, Tlusty D, Todoroki T, Tokarev M, Tomkiel CA, Trentalange S, Tribble RE, Tribedy P, Tripathy SK, Truhlar T, Trzeciak BA, Tsai OD, Tu Z, Ullrich T, Underwood DG, Upsal I, Van Buren G, Vanek J, Vasiliev AN, Vassiliev I, Verkest V, Videbæk F, Vokal S, Voloshin SA, Wang F, Wang G, Wang JS, Wang P, Wang X, Wang Y, Wang Y, Wang Z, Webb JC, Weidenkaff PC, Wen L, Westfall GD, Wieman H, Wissink SW, Wu J, Wu J, Wu Y, Xi B, Xiao ZG, Xie G, Xie W, Xu H, Xu N, Xu QH, Xu Y, Xu Z, Xu Z, Yan G, Yang C, Yang Q, Yang S, Yang Y, Ye Z, Ye Z, Yi L, Yip K, Yu Y, Zbroszczyk H, Zha W, Zhang C, et al. PMID: 36083674.
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    43. Vascular Proteome Responses Precede Organ Dysfunction in a Murine Model of Staphylococcus aureus Bacteremia. mSystems. 2022 08 30; 7(4):e0039522. Sorrentino JT, Golden GJ, Morris C, Painter CD, Nizet V, Campos AR, Smith JW, Karlsson C, Malmström J, Lewis NE, Esko JD, Gómez Toledo A. PMID: 35913192; PMCID: PMC9426442.
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    44. What are housekeeping genes? PLoS Comput Biol. 2022 07; 18(7):e1010295. Joshi CJ, Ke W, Drangowska-Way A, O'Rourke EJ, Lewis NE. PMID: 35830477; PMCID: PMC9312424.
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    45. Non-protective immune imprint underlies failure of Staphylococcus aureus IsdB vaccine. Cell Host Microbe. 2022 08 10; 30(8):1163-1172.e6. Tsai CM, Caldera JR, Hajam IA, Chiang AWT, Tsai CH, Li H, Díez ML, Gonzalez C, Trieu D, Martins GA, Underhill DM, Arditi M, Lewis NE, Liu GY. PMID: 35803276; PMCID: PMC9378590.
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    46. Context-aware deconvolution of cell-cell communication with Tensor-cell2cell. Nat Commun. 2022 06 27; 13(1):3665. Armingol E, Baghdassarian HM, Martino C, Perez-Lopez A, Aamodt C, Knight R, Lewis NE. PMID: 35760817; PMCID: PMC9237099.
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    47. Artificial intelligence in the analysis of glycosylation data. Biotechnol Adv. 2022 11; 60:108008. Li H, Chiang AWT, Lewis NE. PMID: 35738510.
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    48. Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multi-omics integration. Nat Commun. 2022 05 04; 13(1):2455. Kellman BP, Richelle A, Yang JY, Chapla D, Chiang AWT, Najera JA, Liang C, Fürst A, Bao B, Koga N, Mohammad MA, Bruntse AB, Haymond MW, Moremen KW, Bode L, Lewis NE. PMID: 35508452; PMCID: PMC9068700.
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    49. Author Correction: Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate. Nat Chem Biol. 2022 May; 18(5):575. Weiss RJ, Spahn PN, Chiang AWT, Liu Q, Li J, Hamill KM, Rother S, Clausen TM, Hoeksema MA, Timm BM, Godula K, Glass CK, Tor Y, Gordts PLSM, Lewis NE, Esko JD. PMID: 35354934.
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    50. Harnessing secretory pathway differences between HEK293 and CHO to rescue production of difficult to express proteins. Metab Eng. 2022 07; 72:171-187. Malm M, Kuo CC, Barzadd MM, Mebrahtu A, Wistbacka N, Razavi R, Volk AL, Lundqvist M, Kotol D, Tegel H, Hober S, Edfors F, Gräslund T, Chotteau V, Field R, Varley PG, Roth RG, Lewis NE, Hatton D, Rockberg J. PMID: 35301123; PMCID: PMC9189052.
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    51. Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells. Appl Microbiol Biotechnol. 2022 Feb; 106(3):1113-1126. Savizi ISP, Maghsoudi N, Motamedian E, Lewis NE, Shojaosadati SA. PMID: 35044498.
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    52. Multiplex genome editing of mammalian cells for producing recombinant heparin. Metab Eng. 2022 03; 70:155-165. Thacker BE, Thorne KJ, Cartwright C, Park J, Glass K, Chea A, Kellman BP, Lewis NE, Wang Z, Di Nardo A, Sharfstein ST, Jeske W, Walenga J, Hogwood J, Gray E, Mulloy B, Esko JD, Glass CA. PMID: 35038554.
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    53. Correction: StanDep: Capturing transcriptomic variability improves context-specific metabolic models. PLoS Comput Biol. 2022 Jan; 18(1):e1009776. Joshi CJ, Schinn SM, Richelle A, Shamie I, O'Rourke EJ, Lewis NE. PMID: 35007280; PMCID: PMC8746765.
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    54. Restoration of DNA repair mitigates genome instability and increases productivity of Chinese hamster ovary cells. Biotechnol Bioeng. 2022 03; 119(3):963-982. Spahn PN, Zhang X, Hu Q, Lu H, Hamaker NK, Hefzi H, Li S, Kuo CC, Huang Y, Lee JC, Davis AJ, Ly P, Lee KH, Lewis NE. PMID: 34953085; PMCID: PMC8821244.
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    55. Neural responses to affective speech, including motherese, map onto clinical and social eye tracking profiles in toddlers with ASD. Nat Hum Behav. 2022 03; 6(3):443-454. Xiao Y, Wen TH, Kupis L, Eyler LT, Goel D, Vaux K, Lombardo MV, Lewis NE, Pierce K, Courchesne E. PMID: 34980898.
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    56. LIGHT controls distinct homeostatic and inflammatory gene expression profiles in esophageal fibroblasts via differential HVEM and LTβR-mediated mechanisms. Mucosal Immunol. 2022 02; 15(2):327-337. Manresa MC, Wu A, Nhu QM, Chiang AWT, Okamoto K, Miki H, Kurten R, Pham E, Duong LD, Lewis NE, Akuthota P, Croft M, Aceves SS. PMID: 34903876; PMCID: PMC8866113.
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    57. Erratum: An optimized genome-wide, virus-free CRISPR screen for mammalian cells. Cell Rep Methods. 2021 Nov 22; 1(7):100115. Xiong K, Karottki KJC, Hefzi H, Li S, Grav LM, Li S, Spahn P, Lee JS, Ventina I, Lee GM, Lewis NE, Kildegaard HF, Pedersen LE. PMID: 35475003; PMCID: PMC9017133.
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    58. Immune response to intravenous immunoglobulin in patients with Kawasaki disease and MIS-C. J Clin Invest. 2021 10 15; 131(20). Zhu YP, Shamie I, Lee JC, Nowell CJ, Peng W, Angulo S, Le LN, Liu Y, Miao H, Xiong H, Pena CJ, Moreno E, Griffis E, Labou SG, Franco A, Broderick L, Hoffman HM, Shimizu C, Lewis NE, Kanegaye JT, Tremoulet AH, Burns JC, Croker BA, Pediatric Emergency Medicine Kawasaki Disease Research Group Consortium. PMID: 34464357; PMCID: PMC8516453.
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    59. Endothelial Heparan Sulfate Mediates Hepatic Neutrophil Trafficking and Injury during Staphylococcus aureus Sepsis. mBio. 2021 10 26; 12(5):e0118121. Golden GJ, Toledo AG, Marki A, Sorrentino JT, Morris C, Riley RJ, Spliid C, Chen Q, Cornax I, Lewis NE, Varki N, Le D, Malmström J, Karlsson C, Ley K, Nizet V, Esko JD. PMID: 34544271; PMCID: PMC8546592.
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    60. Atypical genomic cortical patterning in autism with poor early language outcome. Sci Adv. 2021 Sep 03; 7(36):eabh1663. Lombardo MV, Eyler L, Pramparo T, Gazestani VH, Hagler DJ, Chen CH, Dale AM, Seidlitz J, Bethlehem RAI, Bertelsen N, Barnes CC, Lopez L, Campbell K, Lewis NE, Pierce K, Courchesne E. PMID: 34516910; PMCID: PMC8442861.
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    61. Synergisms of machine learning and constraint-based modeling of metabolism for analysis and optimization of fermentation parameters. Biotechnol J. 2021 Nov; 16(11):e2100212. Khaleghi MK, Savizi ISP, Lewis NE, Shojaosadati SA. PMID: 34390201.
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    62. Correcting for sparsity and interdependence in glycomics by accounting for glycan biosynthesis. Nat Commun. 2021 08 17; 12(1):4988. Bao B, Kellman BP, Chiang AWT, Zhang Y, Sorrentino JT, York AK, Mohammad MA, Haymond MW, Bode L, Lewis NE. PMID: 34404781; PMCID: PMC8371009.
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    63. An optimized genome-wide, virus-free CRISPR screen for mammalian cells. Cell Rep Methods. 2021 08 23; 1(4). Xiong K, Karottki KJC, Hefzi H, Li S, Grav LM, Li S, Spahn P, Lee JS, Ventina I, Lee GM, Lewis NE, Kildegaard HF, Pedersen LE. PMID: 34935002; PMCID: PMC8687118.
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    64. A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells. NAR Genom Bioinform. 2021 Sep; 3(3):lqab061. Shamie I, Duttke SH, Karottki KJC, Han CZ, Hansen AH, Hefzi H, Xiong K, Li S, Roth SJ, Tao J, Lee GM, Glass CK, Kildegaard HF, Benner C, Lewis NE. PMID: 34268494; PMCID: PMC8276764.
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    65. Model-based assessment of mammalian cell metabolic functionalities using omics data. Cell Rep Methods. 2021 07 26; 1(3). Richelle A, Kellman BP, Wenzel AT, Chiang AWT, Reagan T, Gutierrez JM, Joshi C, Li S, Liu JK, Masson H, Lee J, Li Z, Heirendt L, Trefois C, Juarez EF, Bath T, Borland D, Mesirov JP, Robasky K, Lewis NE. PMID: 34761247; PMCID: PMC8577426.
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    66. Dysregulation of the secretory pathway connects Alzheimer's disease genetics to aggregate formation. Cell Syst. 2021 09 22; 12(9):873-884.e4. Kuo CC, Chiang AWT, Baghdassarian HM, Lewis NE. PMID: 34171228; PMCID: PMC8505362.
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    67. Systems glycobiology for discovering drug targets, biomarkers, and rational designs for glyco-immunotherapy. J Biomed Sci. 2021 Jun 22; 28(1):50. Chiang AWT, Baghdassarian HM, Kellman BP, Bao B, Sorrentino JT, Liang C, Kuo CC, Masson HO, Lewis NE. PMID: 34158025; PMCID: PMC8218521.
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    68. From omics to Cellular mechanisms in mammalian cell factory development. Curr Opin Chem Eng. 2021 Jun; 32. Samoudi M, Masson HO, Kuo CC, Robinson CM, Lewis NE. PMID: 37475722; PMCID: PMC10357924.
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    69. Type 2 Immunity and Age Modify Gene Expression of Coronavirus-induced Disease 2019 Receptors in Eosinophilic Gastrointestinal Disorders. J Pediatr Gastroenterol Nutr. 2021 05 01; 72(5):718-722. Chiang AWT, Duong LD, Shoda T, Nhu QM, Ruffner M, Hara T, Aaron B, Joplin E, Manresa MC, Abonia JP, Dellon ES, Hirano I, Gonsalves N, Gupta SK, Furuta GT, Rothenberg ME, Lewis NE, Muir AB, Aceves SS, CEGIR Investigator Group. PMID: 33394891; PMCID: PMC8048378.
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    70. Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate. Nat Chem Biol. 2021 06; 17(6):684-692. Weiss RJ, Spahn PN, Chiang AWT, Liu Q, Li J, Hamill KM, Rother S, Clausen TM, Hoeksema MA, Timm BM, Godula K, Glass CK, Tor Y, Gordts PLSM, Lewis NE, Esko JD. PMID: 33846619; PMCID: PMC8159865.
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    71. A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes. Metab Eng. 2021 07; 66:114-122. Karottki KJC, Hefzi H, Li S, Pedersen LE, Spahn PN, Joshi C, Ruckerbauer D, Bort JAH, Thomas A, Lee JS, Borth N, Lee GM, Kildegaard HF, Lewis NE. PMID: 33813034; PMCID: PMC8193919.
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    72. Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells. Metab Eng. 2021 07; 66:21-30. Schinn SM, Morrison C, Wei W, Zhang L, Lewis NE. PMID: 33771719.
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    73. Coordinate regulation of systemic and kidney tryptophan metabolism by the drug transporters OAT1 and OAT3. J Biol Chem. 2021 Jan-Jun; 296:100575. Granados JC, Richelle A, Gutierrez JM, Zhang P, Zhang X, Bhatnagar V, Lewis NE, Nigam SK. PMID: 33757768; PMCID: PMC8102410.
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    74. The lytic polysaccharide monooxygenase CbpD promotes Pseudomonas aeruginosa virulence in systemic infection. Nat Commun. 2021 02 23; 12(1):1230. Askarian F, Uchiyama S, Masson H, Sørensen HV, Golten O, Bunæs AC, Mekasha S, Røhr ÅK, Kommedal E, Ludviksen JA, Arntzen MØ, Schmidt B, Zurich RH, van Sorge NM, Eijsink VGH, Krengel U, Mollnes TE, Lewis NE, Nizet V, Vaaje-Kolstad G. PMID: 33623002; PMCID: PMC7902821.
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    75. A genome-scale metabolic network model and machine learning predict amino acid concentrations in Chinese Hamster Ovary cell cultures. Biotechnol Bioeng. 2021 05; 118(5):2118-2123. Schinn SM, Morrison C, Wei W, Zhang L, Lewis NE. PMID: 33580712.
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    76. A unique esophageal extracellular matrix proteome alters normal fibroblast function in severe eosinophilic esophagitis. J Allergy Clin Immunol. 2021 08; 148(2):486-494. Hsieh LY, Chiang AWT, Duong LD, Kuo CC, Dong SX, Dohil R, Kurten R, Lewis NE, Aceves SS. PMID: 33556465; PMCID: PMC8342625.
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    77. A Systems View of the Heparan Sulfate Interactome. J Histochem Cytochem. 2021 02; 69(2):105-119. Gómez Toledo A, Sorrentino JT, Sandoval DR, Malmström J, Lewis NE, Esko JD. PMID: 33494649; PMCID: PMC7841697.
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    78. Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing. BMC Genomics. 2021 Jan 21; 22(1):69. Kellman BP, Baghdassarian HM, Pramparo T, Shamie I, Gazestani V, Begzati A, Li S, Nalabolu S, Murray S, Lopez L, Pierce K, Courchesne E, Lewis NE. PMID: 33478392; PMCID: PMC7818915.
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    79. CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines. PLoS Comput Biol. 2020 12; 16(12):e1008498. Lin D, Yalamanchili HB, Zhang X, Lewis NE, Alves CS, Groot J, Arnsdorf J, Bjørn SP, Wulff T, Voldborg BG, Zhou Y, Zhang B. PMID: 33351794; PMCID: PMC7790544.
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    80. Big-Data Glycomics: Tools to Connect Glycan Biosynthesis to Extracellular Communication. Trends Biochem Sci. 2021 04; 46(4):284-300. Kellman BP, Lewis NE. PMID: 33349503; PMCID: PMC7954846.
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    81. In situ detection of protein interactions for recombinant therapeutic enzymes. Biotechnol Bioeng. 2021 02; 118(2):890-904. Samoudi M, Kuo CC, Robinson CM, Shams-Ud-Doha K, Schinn SM, Kol S, Weiss L, Petersen Bjorn S, Voldborg BG, Rosa Campos A, Lewis NE. PMID: 33169829; PMCID: PMC7855575.
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    82. Deciphering cell-cell interactions and communication from gene expression. Nat Rev Genet. 2021 02; 22(2):71-88. Armingol E, Officer A, Harismendy O, Lewis NE. PMID: 33168968; PMCID: PMC7649713.
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    83. A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR). Beilstein J Org Chem. 2020; 16:2645-2662. Kellman BP, Zhang Y, Logomasini E, Meinhardt E, Godinez-Macias KP, Chiang AWT, Sorrentino JT, Liang C, Bao B, Zhou Y, Akase S, Sogabe I, Kouka T, Winzeler EA, Wilson IBH, Campbell MP, Neelamegham S, Krambeck FJ, Aoki-Kinoshita KF, Lewis NE. PMID: 33178355; PMCID: PMC7607430.
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    84. Systematically gap-filling the genome-scale metabolic model of CHO cells. Biotechnol Lett. 2021 Jan; 43(1):73-87. Fouladiha H, Marashi SA, Li S, Li Z, Masson HO, Vaziri B, Lewis NE. PMID: 33040240.
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    85. Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor. Cell Host Microbe. 2020 10 07; 28(4):586-601.e6. Zhao P, Praissman JL, Grant OC, Cai Y, Xiao T, Rosenbalm KE, Aoki K, Kellman BP, Bridger R, Barouch DH, Brindley MA, Lewis NE, Tiemeyer M, Chen B, Woods RJ, Wells L. PMID: 32841605; PMCID: PMC7443692.
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    86. Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity. bioRxiv. 2020 Aug 18. Martino C, Kellman BP, Sandoval DR, Clausen TM, Marotz CA, Song SJ, Wandro S, Zaramela LS, Salido Benítez RA, Zhu Q, Armingol E, Vázquez-Baeza Y, McDonald D, Sorrentino JT, Taylor B, Belda-Ferre P, Liang C, Zhang Y, Schifanella L, Klatt NR, Havulinna AS, Jousilahti P, Huang S, Haiminen N, Parida L, Kim HC, Swafford AD, Zengler K, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Esko JD, Lewis NE, Knight R. PMID: 32839779; PMCID: PMC7444296.
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    87. Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor. bioRxiv. 2020 Jul 24. Zhao P, Praissman JL, Grant OC, Cai Y, Xiao T, Rosenbalm KE, Aoki K, Kellman BP, Bridger R, Barouch DH, Brindley MA, Lewis NE, Tiemeyer M, Chen B, Woods RJ, Wells L. PMID: 32743578; PMCID: PMC7386495.
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    88. Increased Production of LIGHT by T Cells in Eosinophilic Esophagitis Promotes Differentiation of Esophageal Fibroblasts Toward an Inflammatory Phenotype. Gastroenterology. 2020 11; 159(5):1778-1792.e13. Manresa MC, Chiang AWT, Kurten RC, Dohil R, Brickner H, Dohil L, Herro R, Akuthota P, Lewis NE, Croft M, Aceves SS. PMID: 32712105; PMCID: PMC7726704.
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    89. What CHO is made of: Variations in the biomass composition of Chinese hamster ovary cell lines. Metab Eng. 2020 09; 61:288-300. Széliová D, Ruckerbauer DE, Galleguillos SN, Petersen LB, Natter K, Hanscho M, Troyer C, Causon T, Schoeny H, Christensen HB, Lee DY, Lewis NE, Koellensperger G, Hann S, Nielsen LK, Borth N, Zanghellini J. PMID: 32619503.
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    90. Dietary serine-microbiota interaction enhances chemotherapeutic toxicity without altering drug conversion. Nat Commun. 2020 05 22; 11(1):2587. Ke W, Saba JA, Yao CH, Hilzendeger MA, Drangowska-Way A, Joshi C, Mony VK, Benjamin SB, Zhang S, Locasale J, Patti GJ, Lewis N, O'Rourke EJ. PMID: 32444616; PMCID: PMC7244588.
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    91. StanDep: Capturing transcriptomic variability improves context-specific metabolic models. PLoS Comput Biol. 2020 05; 16(5):e1007764. Joshi CJ, Schinn SM, Richelle A, Shamie I, O'Rourke EJ, Lewis NE. PMID: 32396573; PMCID: PMC7244210.
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    92. Multiplex secretome engineering enhances recombinant protein production and purity. Nat Commun. 2020 04 20; 11(1):1908. Kol S, Ley D, Wulff T, Decker M, Arnsdorf J, Schoffelen S, Hansen AH, Jensen TL, Gutierrez JM, Chiang AWT, Masson HO, Palsson BO, Voldborg BG, Pedersen LE, Kildegaard HF, Lee GM, Lewis NE. PMID: 32313013; PMCID: PMC7170862.
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    93. Prenatal Origins of ASD: The When, What, and How of ASD Development. Trends Neurosci. 2020 05; 43(5):326-342. Courchesne E, Gazestani VH, Lewis NE. PMID: 32353336; PMCID: PMC7373219.
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    94. ZNF263 is a transcriptional regulator of heparin and heparan sulfate biosynthesis. Proc Natl Acad Sci U S A. 2020 04 28; 117(17):9311-9317. Weiss RJ, Spahn PN, Toledo AG, Chiang AWT, Kellman BP, Li J, Benner C, Glass CK, Gordts PLSM, Lewis NE, Esko JD. PMID: 32277030; PMCID: PMC7196839.
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    95. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020 Apr; 38(4):504. Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Sheriff RSM, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. PMID: 32265554; PMCID: PMC7138757.
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    96. A metabolic network-based approach for developing feeding strategies for CHO cells to increase monoclonal antibody production. Bioprocess Biosyst Eng. 2020 Aug; 43(8):1381-1389. Fouladiha H, Marashi SA, Torkashvand F, Mahboudi F, Lewis NE, Vaziri B. PMID: 32211960.
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    97. MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020 03; 38(3):272-276. Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Malik Sheriff RS, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. PMID: 32123384; PMCID: PMC7082222.
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    98. A Markov model of glycosylation elucidates isozyme specificity and glycosyltransferase interactions for glycoengineering. Curr Res Biotechnol. 2020 Nov; 2:22-36. Liang C, Chiang AWT, Hansen AH, Arnsdorf J, Schoffelen S, Sorrentino JT, Kellman BP, Bao B, Voldborg BG, Lewis NE. PMID: 32285041; PMCID: PMC7153765.
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    99. Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion. Nat Commun. 2020 01 02; 11(1):68. Gutierrez JM, Feizi A, Li S, Kallehauge TB, Hefzi H, Grav LM, Ley D, Baycin Hizal D, Betenbaugh MJ, Voldborg B, Faustrup Kildegaard H, Min Lee G, Palsson BO, Nielsen J, Lewis NE. PMID: 31896772; PMCID: PMC6940358.
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    100. Ptpn6 inhibits caspase-8- and Ripk3/Mlkl-dependent inflammation. Nat Immunol. 2020 01; 21(1):54-64. Speir M, Nowell CJ, Chen AA, O'Donnell JA, Shamie IS, Lakin PR, D'Cruz AA, Braun RO, Babon JJ, Lewis RS, Bliss-Moreau M, Shlomovitz I, Wang S, Cengia LH, Stoica AI, Hakem R, Kelliher MA, O'Reilly LA, Patsiouras H, Lawlor KE, Weller E, Lewis NE, Roberts AW, Gerlic M, Croker BA. PMID: 31819256; PMCID: PMC6923591.
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    101. Awakening dormant glycosyltransferases in CHO cells with CRISPRa. Biotechnol Bioeng. 2020 02; 117(2):593-598. Karottki KJC, Hefzi H, Xiong K, Shamie I, Hansen AH, Li S, Pedersen LE, Li S, Lee JS, Lee GM, Kildegaard HF, Lewis NE. PMID: 31631317; PMCID: PMC7261405.
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    102. Proteomic atlas of organ vasculopathies triggered by Staphylococcus aureus sepsis. Nat Commun. 2019 10 11; 10(1):4656. Toledo AG, Golden G, Campos AR, Cuello H, Sorrentino J, Lewis N, Varki N, Nizet V, Smith JW, Esko JD. PMID: 31604940; PMCID: PMC6789120.
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    103. Increased mAb production in amplified CHO cell lines is associated with increased interaction of CREB1 with transgene promoter. Curr Res Biotechnol. 2019 Nov; 1:49-57. Dahodwala H, Kaushik P, Tejwani V, Kuo CC, Menard P, Henry M, Voldborg BG, Lewis NE, Meleady P, Sharfstein ST. PMID: 32577618; PMCID: PMC7311070.
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    104. A perturbed gene network containing PI3K-AKT, RAS-ERK and WNT-β-catenin pathways in leukocytes is linked to ASD genetics and symptom severity. Nat Neurosci. 2019 10; 22(10):1624-1634. Gazestani VH, Pramparo T, Nalabolu S, Kellman BP, Murray S, Lopez L, Pierce K, Courchesne E, Lewis NE. PMID: 31551593; PMCID: PMC6764590.
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    105. Assessing key decisions for transcriptomic data integration in biochemical networks. PLoS Comput Biol. 2019 07; 15(7):e1007185. Richelle A, Joshi C, Lewis NE. PMID: 31323017; PMCID: PMC6668847.
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    106. Combating viral contaminants in CHO cells by engineering innate immunity. Sci Rep. 2019 06 20; 9(1):8827. Chiang AWT, Li S, Kellman BP, Chattopadhyay G, Zhang Y, Kuo CC, Gutierrez JM, Ghazi F, Schmeisser H, Ménard P, Bjørn SP, Voldborg BG, Rosenberg AS, Puig M, Lewis NE. PMID: 31222165; PMCID: PMC6586939.
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    107. Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements. J Proteome Res. 2019 06 07; 18(6):2433-2445. Li S, Cha SW, Heffner K, Hizal DB, Bowen MA, Chaerkady R, Cole RN, Tejwani V, Kaushik P, Henry M, Meleady P, Sharfstein ST, Betenbaugh MJ, Bafna V, Lewis NE. PMID: 31020842; PMCID: PMC6571120.
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    108. Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions. PLoS Comput Biol. 2019 04; 15(4):e1006867. Richelle A, Chiang AWT, Kuo CC, Lewis NE. PMID: 30986217; PMCID: PMC6483243.
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    109. A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma. Cell. 2019 04 18; 177(3):572-586.e22. Lytle NK, Ferguson LP, Rajbhandari N, Gilroy K, Fox RG, Deshpande A, Schürch CM, Hamilton M, Robertson N, Lin W, Noel P, Wartenberg M, Zlobec I, Eichmann M, Galván JA, Karamitopoulou E, Gilderman T, Esparza LA, Shima Y, Spahn P, French R, Lewis NE, Fisch KM, Sasik R, Rosenthal SB, Kritzik M, Von Hoff D, Han H, Ideker T, Deshpande AJ, Lowy AM, Adams PD, Reya T. PMID: 30955884; PMCID: PMC6711371.
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    110. From Genotype to Phenotype: Augmenting Deep Learning with Networks and Systems Biology. Curr Opin Syst Biol. 2019 Jun; 15:68-73. Gazestani VH, Lewis NE. PMID: 31777764; PMCID: PMC6880750.
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    111. Reduced apoptosis in Chinese hamster ovary cells via optimized CRISPR interference. Biotechnol Bioeng. 2019 07; 116(7):1813-1819. Xiong K, Marquart KF, la Cour Karottki KJ, Li S, Shamie I, Lee JS, Gerling S, Yeo NC, Chavez A, Lee GM, Lewis NE, Kildegaard HF. PMID: 30883679; PMCID: PMC6545153.
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    112. Mitigating Clonal Variation in Recombinant Mammalian Cell Lines. Trends Biotechnol. 2019 09; 37(9):931-942. Lee JS, Kildegaard HF, Lewis NE, Lee GM. PMID: 30898338.
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    113. Systematic Evaluation of Site-Specific Recombinant Gene Expression for Programmable Mammalian Cell Engineering. ACS Synth Biol. 2019 04 19; 8(4):758-774. Pristovšek N, Nallapareddy S, Grav LM, Hefzi H, Lewis NE, Rugbjerg P, Hansen HG, Lee GM, Andersen MR, Kildegaard HF. PMID: 30807689.
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    114. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nat Protoc. 2019 03; 14(3):639-702. Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, Aurich MK, Clancy CM, Modamio J, Sauls JT, Noronha A, Bordbar A, Cousins B, El Assal DC, Valcarcel LV, Apaolaza I, Ghaderi S, Ahookhosh M, Ben Guebila M, Kostromins A, Sompairac N, Le HM, Ma D, Sun Y, Wang L, Yurkovich JT, Oliveira MAP, Vuong PT, El Assal LP, Kuperstein I, Zinovyev A, Hinton HS, Bryant WA, Aragón Artacho FJ, Planes FJ, Stalidzans E, Maass A, Vempala S, Hucka M, Saunders MA, Maranas CD, Lewis NE, Sauter T, Palsson BØ, Thiele I, Fleming RMT. PMID: 30787451; PMCID: PMC6635304.
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    115. Dual RNA-seq identifies human mucosal immunity protein Mucin-13 as a hallmark of Plasmodium exoerythrocytic infection. Nat Commun. 2019 01 30; 10(1):488. LaMonte GM, Orjuela-Sanchez P, Calla J, Wang LT, Li S, Swann J, Cowell AN, Zou BY, Abdel-Haleem Mohamed AM, Villa Galarce ZH, Moreno M, Tong Rios C, Vinetz JM, Lewis N, Winzeler EA. PMID: 30700707; PMCID: PMC6353872.
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    116. Evolution of the exclusively human pathogen Neisseria gonorrhoeae: Human-specific engagement of immunoregulatory Siglecs. Evol Appl. 2019 Feb; 12(2):337-349. Landig CS, Hazel A, Kellman BP, Fong JJ, Schwarz F, Agarwal S, Varki N, Massari P, Lewis NE, Ram S, Varki A. PMID: 30697344; PMCID: PMC6346652.
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    117. Large-scale associations between the leukocyte transcriptome and BOLD responses to speech differ in autism early language outcome subtypes. Nat Neurosci. 2018 12; 21(12):1680-1688. Lombardo MV, Pramparo T, Gazestani V, Warrier V, Bethlehem RAI, Carter Barnes C, Lopez L, Lewis NE, Eyler L, Pierce K, Courchesne E. PMID: 30482947; PMCID: PMC6445349.
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    118. Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans. Front Mol Biosci. 2018; 5:96. 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. PMID: 30488036; PMCID: PMC6246695.
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    119. Revealing Key Determinants of Clonal Variation in Transgene Expression in Recombinant CHO Cells Using Targeted Genome Editing. ACS Synth Biol. 2018 12 21; 7(12):2867-2878. Lee JS, Park JH, Ha TK, Samoudi M, Lewis NE, Palsson BO, Kildegaard HF, Lee GM. PMID: 30388888; PMCID: PMC6535434.
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    120. Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. Proc Natl Acad Sci U S A. 2018 10 23; 115(43):11096-11101. 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. PMID: 30301795; PMCID: PMC6205427.
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    121. Minimizing Clonal Variation during Mammalian Cell Line Engineering for Improved Systems Biology Data Generation. ACS Synth Biol. 2018 09 21; 7(9):2148-2159. Grav LM, Sergeeva D, Lee JS, Marin de Mas I, Lewis NE, Andersen MR, Nielsen LK, Lee GM, Kildegaard HF. PMID: 30060646.
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    122. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods. 2018 Aug; 15(8):611-616. 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. PMID: 30013045; PMCID: PMC6129399.
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    123. The ASD Living Biology: from cell proliferation to clinical phenotype. Mol Psychiatry. 2019 01; 24(1):88-107. Courchesne E, Pramparo T, Gazestani VH, Lombardo MV, Pierce K, Lewis NE. PMID: 29934544; PMCID: PMC6309606.
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    124. A reference genome of the Chinese hamster based on a hybrid assembly strategy. Biotechnol Bioeng. 2018 08; 115(8):2087-2100. 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. PMID: 29704459; PMCID: PMC6045439.
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    125. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. PLoS Comput Biol. 2018 01; 14(1):e1005895. Abdel-Haleem AM, Hefzi H, Mineta K, Gao X, Gojobori T, Palsson BO, Lewis NE, Jamshidi N. PMID: 29300748; PMCID: PMC5771636.
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    126. The emerging role of systems biology for engineering protein production in CHO cells. Curr Opin Biotechnol. 2018 06; 51:64-69. Kuo CC, Chiang AW, Shamie I, Samoudi M, Gutierrez JM, Lewis NE. PMID: 29223005; PMCID: PMC5988649.
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    127. PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens. Sci Rep. 2017 Nov 20; 7(1):15854. Spahn PN, Bath T, Weiss RJ, Kim J, Esko JD, Lewis NE, Harismendy O. PMID: 29158538; PMCID: PMC5696473.
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    128. The Emerging Facets of Non-Cancerous Warburg Effect. Front Endocrinol (Lausanne). 2017; 8:279. Abdel-Haleem AM, Lewis NE, Jamshidi N, Mineta K, Gao X, Gojobori T. PMID: 29109698; PMCID: PMC5660072.
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    129. Hierarchical cortical transcriptome disorganization in autism. Mol Autism. 2017; 8:29. Lombardo MV, Courchesne E, Lewis NE, Pramparo T. PMID: 28649314; PMCID: PMC5480153.
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    130. Improvements in protein production in mammalian cells from targeted metabolic engineering. Curr Opin Syst Biol. 2017 Dec; 6:1-6. Richelle A, Lewis NE. PMID: 29104947; PMCID: PMC5663301.
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    131. Human milk oligosaccharide composition predicts risk of necrotising enterocolitis in preterm infants. Gut. 2018 06; 67(6):1064-1070. Autran CA, Kellman BP, Kim JH, Asztalos E, Blood AB, Spence ECH, Patel AL, Hou J, Lewis NE, Bode L. PMID: 28381523.
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    132. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017 Jun; 14(6):573-576. 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. PMID: 28319113; PMCID: PMC5449203.
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    133. A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models. Cell Syst. 2017 03 22; 4(3):318-329.e6. Opdam S, Richelle A, Kellman B, Li S, Zielinski DC, Lewis NE. PMID: 28215528; PMCID: PMC5526624.
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    134. Ribosome profiling-guided depletion of an mRNA increases cell growth rate and protein secretion. Sci Rep. 2017 01 16; 7:40388. Kallehauge TB, Li S, Pedersen LE, Ha TK, Ley D, Andersen MR, Kildegaard HF, Lee GM, Lewis NE. PMID: 28091612; PMCID: PMC5238448.
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    135. Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion. mBio. 2017 01 10; 8(1). 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. PMID: 28074024; PMCID: PMC5225314.
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    136. Predictive glycoengineering of biosimilars using a Markov chain glycosylation model. Biotechnol J. 2017 Feb; 12(2). Spahn PN, Hansen AH, Kol S, Voldborg BG, Lewis NE. PMID: 27860290; PMCID: PMC5293603.
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    137. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Syst. 2016 11 23; 3(5):434-443.e8. 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. PMID: 27883890; PMCID: PMC5132346.
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    138. Modulating carbohydrate-protein interactions through glycoengineering of monoclonal antibodies to impact cancer physiology. Curr Opin Struct Biol. 2016 10; 40:104-111. Chiang AW, Li S, Spahn PN, Richelle A, Kuo CC, Samoudi M, Lewis NE. PMID: 27639240; PMCID: PMC5161599.
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    139. Recon 2.2: from reconstruction to model of human metabolism. Metabolomics. 2016; 12:109. 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. PMID: 27358602; PMCID: PMC4896983.
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    140. Characterizing the effect of multiple Fc glycan attributes on the effector functions and FcγRIIIa receptor binding activity of an IgG1 antibody. Biotechnol Prog. 2016 09; 32(5):1181-1192. Pace D, Lewis N, Wu T, Gillespie R, Leiske D, Velayudhan J, Rohrbach A, Connell-Crowley L. PMID: 27160519.
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    141. Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis. Genome Med. 2016 Mar 31; 8(1):34. Huang S, Chong N, Lewis NE, Jia W, Xie G, Garmire LX. PMID: 27036109; PMCID: PMC4818393.
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    142. 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. Golabgir A, Gutierrez JM, Hefzi H, Li S, Palsson BO, Herwig C, Lewis NE. PMID: 26948029.
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    143. Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers. Mol Syst Biol. 2015 Dec 14; 11(12):841. Pramparo T, Lombardo MV, Campbell K, Barnes CC, Marinero S, Solso S, Young J, Mayo M, Dale A, Ahrens-Barbeau C, Murray SS, Lopez L, Lewis N, Pierce K, Courchesne E. PMID: 26668231; PMCID: PMC4704485.
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    144. A Markov chain model for N-linked protein glycosylation--towards a low-parameter tool for model-driven glycoengineering. Metab Eng. 2016 Jan; 33:52-66. Spahn PN, Hansen AH, Hansen HG, Arnsdorf J, Kildegaard HF, Lewis NE. PMID: 26537759; PMCID: PMC5031499.
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    145. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res. 2016 Jan 04; 44(D1):D515-22. King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE. PMID: 26476456; PMCID: PMC4702785.
      View in: PubMed   Mentions: 322     Fields:    
    146. Do genome-scale models need exact solvers or clearer standards? Mol Syst Biol. 2015 Oct 14; 11(10):831. 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. PMID: 26467284; PMCID: PMC4631202.
      View in: PubMed   Mentions: 32     Fields:    
    147. Elucidation of the CHO Super-Ome (CHO-SO) by Proteoinformatics. J Proteome Res. 2015 Nov 06; 14(11):4687-703. 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. PMID: 26418914; PMCID: PMC4721571.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    148. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput Biol. 2015 Aug; 11(8):e1004321. King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO. PMID: 26313928; PMCID: PMC4552468.
      View in: PubMed   Mentions: 141     Fields:    Translation:Cells
    149. Systems analysis of host-parasite interactions. Wiley Interdiscip Rev Syst Biol Med. 2015 Nov-Dec; 7(6):381-400. Swann J, Jamshidi N, Lewis NE, Winzeler EA. PMID: 26306749; PMCID: PMC4679367.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimals
    150. Differential binding of heavy chain variable domain 3 antigen binding fragments to protein A chromatography resins. J Chromatogr A. 2015 Aug 28; 1409:60-9. Bach J, Lewis N, Maggiora K, Gillespie AJ, Connell-Crowley L. PMID: 26189670.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    151. Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling. Biotechnol J. 2015 Jul; 10(7):939-49. Gutierrez JM, Lewis NE. PMID: 26099571.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    152. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics. 2015 Oct 15; 31(20):3383-6. 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. PMID: 26079347; PMCID: PMC4595895.
      View in: PubMed   Mentions: 16     Fields:    
    153. CRISPR/Cas9-mediated genome engineering of CHO cell factories: Application and perspectives. Biotechnol J. 2015 Jul; 10(7):979-94. Lee JS, Grav LM, Lewis NE, Faustrup Kildegaard H. PMID: 26058577.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    154. Rapid neurogenesis through transcriptional activation in human stem cells. Mol Syst Biol. 2014 Nov 17; 10:760. 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. PMID: 25403753; PMCID: PMC4299601.
      View in: PubMed   Mentions: 114     Fields:    Translation:HumansCells
    155. Systems glycobiology for glycoengineering. Curr Opin Biotechnol. 2014 Dec; 30:218-24. Spahn PN, Lewis NE. PMID: 25202878.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    156. Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice. PLoS One. 2014; 9(7):e102319. Kumar A, Harrelson T, Lewis NE, Gallagher EJ, LeRoith D, Shiloach J, Betenbaugh MJ. PMID: 25029527; PMCID: PMC4100879.
      View in: PubMed   Mentions: 9     Fields:    Translation:Animals
    157. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Mol Syst Biol. 2014 Jul 01; 10:737. Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO. PMID: 24987116; PMCID: PMC4299494.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    158. The role of replicates for error mitigation in next-generation sequencing. Nat Rev Genet. 2014 01; 15(1):56-62. Robasky K, Lewis NE, Church GM. PMID: 24322726; PMCID: PMC4103745.
      View in: PubMed   Mentions: 140     Fields:    Translation:Humans
    159. The evolution of genome-scale models of cancer metabolism. Front Physiol. 2013 Sep 03; 4:237. Lewis NE, Abdel-Haleem AM. PMID: 24027532; PMCID: PMC3759783.
      View in: PubMed   Mentions: 43  
    160. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nat Biotechnol. 2013 Aug; 31(8):759-65. 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. PMID: 23873082.
      View in: PubMed   Mentions: 96     Fields:    Translation:HumansAnimalsCells
    161. The emerging CHO systems biology era: harnessing the 'omics revolution for biotechnology. Curr Opin Biotechnol. 2013 Dec; 24(6):1102-7. Kildegaard HF, Baycin-Hizal D, Lewis NE, Betenbaugh MJ. PMID: 23523260.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansAnimalsCells
    162. Analysis of omics data with genome-scale models of metabolism. Mol Biosyst. 2013 Feb 02; 9(2):167-74. Hyduke DR, Lewis NE, Palsson BØ. PMID: 23247105; PMCID: PMC3594511.
      View in: PubMed   Mentions: 79     Fields:    Translation:HumansAnimals
    163. A proof for loop-law constraints in stoichiometric metabolic networks. BMC Syst Biol. 2012 Nov 12; 6:140. Noor E, Lewis NE, Milo R. PMID: 23146116; PMCID: PMC3560238.
      View in: PubMed   Mentions: 9     Fields:    
    164. Proteomic analysis of Chinese hamster ovary cells. J Proteome Res. 2012 Nov 02; 11(11):5265-76. 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. PMID: 22971049; PMCID: PMC3772721.
      View in: PubMed   Mentions: 59     Fields:    Translation:AnimalsCells
    165. Network context and selection in the evolution to enzyme specificity. Science. 2012 Aug 31; 337(6098):1101-4. Nam H, Lewis NE, Lerman JA, Lee DH, Chang RL, Kim D, Palsson BO. PMID: 22936779; PMCID: PMC3536066.
      View in: PubMed   Mentions: 114     Fields:    Translation:Cells
    166. In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun. 2012 Jul 03; 3:929. Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. PMID: 22760628; PMCID: PMC3827721.
      View in: PubMed   Mentions: 119     Fields:    Translation:Cells
    167. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol. 2012 Feb 27; 10(4):291-305. Lewis NE, Nagarajan H, Palsson BO. PMID: 22367118; PMCID: PMC3536058.
      View in: PubMed   Mentions: 327     Fields:    Translation:Cells
    168. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc. 2011 Aug 04; 6(9):1290-307. 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. PMID: 21886097; PMCID: PMC3319681.
      View in: PubMed   Mentions: 580     Fields:    
    169. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nat Biotechnol. 2011 Jul 31; 29(8):735-41. 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. PMID: 21804562; PMCID: PMC3164356.
      View in: PubMed   Mentions: 229     Fields:    Translation:AnimalsCells
    170. Microbial laboratory evolution in the era of genome-scale science. Mol Syst Biol. 2011 Jul 05; 7:509. Conrad TM, Lewis NE, Palsson BØ. PMID: 21734648; PMCID: PMC3159978.
      View in: PubMed   Mentions: 129     Fields:    Translation:Cells
    171. The role of cellular objectives and selective pressures in metabolic pathway evolution. Curr Opin Biotechnol. 2011 Aug; 22(4):595-600. Nam H, Conrad TM, Lewis NE. PMID: 21481583; PMCID: PMC3173765.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    172. Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys J. 2011 Feb 02; 100(3):544-553. Schellenberger J, Lewis NE, Palsson BØ. PMID: 21281568; PMCID: PMC3030201.
      View in: PubMed   Mentions: 94     Fields:    Translation:Cells
    173. Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nat Biotechnol. 2010 Dec; 28(12):1279-85. Lewis NE, Schramm G, Bordbar A, Schellenberger J, Andersen MP, Cheng JK, Patel N, Yee A, Lewis RA, Eils R, König R, Palsson BØ. PMID: 21102456; PMCID: PMC3140076.
      View in: PubMed   Mentions: 123     Fields:    Translation:Humans
    174. 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 23; 107(47):20500-5. Conrad TM, Frazier M, Joyce AR, Cho BK, Knight EM, Lewis NE, Landick R, Palsson BØ. PMID: 21057108; PMCID: PMC2996682.
      View in: PubMed   Mentions: 110     Fields:    Translation:Cells
    175. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol Syst Biol. 2010 Oct 19; 6:422. Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N. PMID: 20959820; PMCID: PMC2990636.
      View in: PubMed   Mentions: 132     Fields:    Translation:HumansCells
    176. Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655. Appl Environ Microbiol. 2010 Oct; 76(19):6529-40. Portnoy VA, Scott DA, Lewis NE, Tarasova Y, Osterman AL, Palsson BØ. PMID: 20709841; PMCID: PMC2950451.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    177. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol. 2010 Jul; 6:390. 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. PMID: 20664636; PMCID: PMC2925526.
      View in: PubMed   Mentions: 289     Fields:    Translation:Cells
    178. Design and analysis of synthetic carbon fixation pathways. Proc Natl Acad Sci U S A. 2010 May 11; 107(19):8889-94. Bar-Even A, Noor E, Lewis NE, Milo R. PMID: 20410460; PMCID: PMC2889323.
      View in: PubMed   Mentions: 140     Fields:    Translation:Cells
    179. 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; 191(11):3437-44. Lewis NE, Cho BK, Knight EM, Palsson BO. PMID: 19363119; PMCID: PMC2681886.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    180. Analysis of low-abundance, low-molecular-weight serum proteins using mass spectrometry. J Biomol Tech. 2004 Dec; 15(4):238-48. Merrell K, Southwick K, Graves SW, Esplin MS, Lewis NE, Thulin CD. PMID: 15585820; PMCID: PMC2291707.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansAnimalsCells
    181. The risk of seizures after receipt of whole-cell pertussis or measles, mumps, and rubella vaccine. N Engl J Med. 2001 Aug 30; 345(9):656-61. Barlow WE, Davis RL, Glasser JW, Rhodes PH, Thompson RS, Mullooly JP, Black SB, Shinefield HR, Ward JI, Marcy SM, DeStefano F, Chen RT, Immanuel V, Pearson JA, Vadheim CM, Rebolledo V, Christakis D, Benson PJ, Lewis N, Centers for Disease Control and Prevention Vaccine Safety Datalink Working Group. PMID: 11547719.
      View in: PubMed   Mentions: 66     Fields:    Translation:Humans
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