Publications

2022

Multi-omics analysis of Dsup expressing human cells reveals open chromatin architectural dynamics underyling radioprotection.

Westover C, Najjar D, Meydan C, Grigorev K, Veling MT, Chang RL, Chin C, Butler D, Afshin EE, Silver P, Mason C✉. bioRxiv. 2022, Mar 27; doi: https://doi.org/10.1101/2020.11.10.373571.

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High content screening and computational prediction reveal viral genes that suppress innate immune response.

Ng T, Olson E, Yoo TY, Weiss HS, Koide Y, Koch P, Rollins N, Mach P, Meisinger T, Bricken T, Chang T, Molloy C, Zürcher J, Chang RL, Mitchison T, Glass J, Marks D, Way J, and Silver P
mSystems. 2022, Mar 23; e0146621. doi: 10.1128/msystems.01466-21.

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Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells.

Veling MT*, Nguyen DT*, Thadani NN, Oster ME, Rollins NJ, Brock KP, Bethel NP, Lim S, Baker D, Way JC, Marks DS, Chang RL✉, Silver PA✉. ACS Synth Biol. 2022, Feb 18; doi: https://doi.org/10.1021/acssynbio.1c00572.

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Making sense of disorder: Investigating intrinsically disordered proteins in the tardigrade proteome via a computational approach.

Lowe NE, Chang RL✉. bioRxiv. 2022, Jan 31; doi: https://doi.org/10.1101/2022.01.29.478329.

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2020

Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage.

Chang RL✉, Stanley JA, Robinson MC, Sher JW, Li Z, Chan YA, Omdahl AR, Wattiez R, Godzik A, Matallana-Surget S✉. EMBO J. 2020, Oct 19; e104523. doi: 10.15252/embj.2020104523.

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2018

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.

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2016

Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation.

Chaiboonchoe A*, Ghamsari L*, Dohai B*, Ng P*, Khraiwesh B, Jaiswal A, Jijakli K, Koussa J, Nelson DR, Cai H, Yang X, Chang RL, Papin J✉, Yu H✉, Balaji S✉, Salehi-Ashtiani K✉. Mol Biosyst. 2016, Jul 19; 12(8):2394-407.
 

Systems biology of the structural proteome.

Brunk E*, Mih N*, Monk J, Zhang Z, O’Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO✉. BMC Syst Biol. 2016, Mar 11; 10:26.
 

Streptomyces thermoautotrophicus does not fix nitrogen.

MacKellar D, Lieber L, Norman JS, Bolger A, Tobin C, Murray JW, Oksaksin M, Chang RL, Ford TJ, Nguyen PQ, Woodward J, Permingeat HR, Joshi NS, Silver PA, Usadel B, Rutherford AW, Friesen ML, Prell J✉. Sci Rep. 2016, Feb 1; 6:20086.

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2015

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 RMT, 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 BØ, 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.
 

Transplantability of a circadian clock to a noncircadian organism.

Chen AH, Lubkowicz D, Yeong V, Chang RL, Silver PA✉. Sci. Adv. 2015, Jun 1; 1(5):e1500358.

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2013

Antibacterial mechanisms identified through structural systems pharmacology.

Chang RL, Xie L, Bourne PE, Palsson BØ✉. BMC Syst Biol. 2013, Oct 10; 7:102.
 

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction.

O’Brien ET*, Lerman JA*, Chang RL, Hyduke DR, Palsson BØ✉. Mol Syst Biol. 2013, Oct 1; 9:693.
 

Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli.

Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BØ✉. Science. 2013, Jun 7; 340(6137):1220-1223.

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2012

Network context and selection in the evolution to enzyme specificity.

Nam H*, Lewis NE*, Lerman JA, Lee D, Chang RL, Kim D, Palsson BO✉. Science. 2012, Aug 31; 337(6098):1101-1104.

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2011

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.

Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K✉, Papin JA✉. Mol Syst Biol. 2011, Aug 2; 7:518.

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2010

Drug off-target effects predicted using structural analysis in the context of a metabolic network model.

Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ✉. PLoS Comput Biol. 2010, Sep 23; 6(9):e1000938.
 

Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks.

Chang RL, Luo F, Johnson S, Scheuermann RH✉. Int J Bioinform Res Appl. 2010; 6(2):101-19.

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2009

Metabolic network analysis integrated with transcript verification for sequenced genomes.

Manichaikul A*, Ghamsari L*, Hom EFY*, Lin C*, Murray RR*, Chang RL*, Balaji S, Hao T, Shen Y, Chavali AK, Thiele I, Yang X, Mello E, Hill DE, Vidal M, Salehi-Ashtiani K✉, Papin JA✉. Nat Methods 2009, Aug; 6(8):589-92.

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2008

BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence.

Squires B, Macken C, Garcia-Sastre A, Godbole S, Noronha J, Hunt V, Chang RL, Larsen CN, Klem E, Biersack K, Scheuermann RH✉. Nucleic Acids Res. 2008, Jan; 36(Database issue):D497-503.

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2007

Modular organization of protein interaction networks.

Luo F✉, Yang Y, Chen CF, Chang RL, Zhou J, Scheuermann RH. Bioinformatics 2007, Jan 15; 23(2):207-214.

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