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Items: 45

1.

Improving designer glycan production in Escherichia coli through model-guided metabolic engineering.

Wayman JA, Glasscock C, Mansell TJ, DeLisa MP, Varner JD.

Metab Eng Commun. 2019 Mar 29;9:e00088. doi: 10.1016/j.mec.2019.e00088. eCollection 2019 Dec.

2.

Analysis of the role of thrombomodulin in all-trans retinoic acid treatment of coagulation disorders in cancer patients.

Ghaffari H, Varner JD, Petzold LR.

Theor Biol Med Model. 2019 Feb 14;16(1):3. doi: 10.1186/s12976-019-0099-z.

3.

Retinoic acid and 6-formylindolo(3,2-b)carbazole (FICZ) combination therapy reveals putative targets for enhancing response in non-APL AML.

Bunaciu RP, MacDonald RJ, Jensen HA, Gao F, Wang X, Johnson L, Varner JD, Yen A.

Leuk Lymphoma. 2019 Jul;60(7):1697-1708. doi: 10.1080/10428194.2018.1543880. Epub 2018 Dec 20.

PMID:
30570341
4.

Multi-scale computational study of the Warburg effect, reverse Warburg effect and glutamine addiction in solid tumors.

Shan M, Dai D, Vudem A, Varner JD, Stroock AD.

PLoS Comput Biol. 2018 Dec 7;14(12):e1006584. doi: 10.1371/journal.pcbi.1006584. eCollection 2018 Dec.

5.

Correction to: Recurrence of nephrotic syndrome following kidney transplantation is associated with initial native kidney biopsy findings : A Midwest Pediatric Nephrology Consortium (MWPNC) study.

Pelletier JH, Kumar KR, Engen R, Bensimhon A, Varner JD, Rheault MN, Srivastava T, Straatmann C, Silva C, Davis TK, Wenderfer SE, Gibson K, Selewski D, Barcia J, Weng P, Licht C, Jawa N, Kallash M, Foreman JW, Wigfall DR, Chua AN, Chambers E, Hornik CP, Brewer ED, Nagaraj SK, Greenbaum LA, Gbadegesin RA.

Pediatr Nephrol. 2019 Mar;34(3):539. doi: 10.1007/s00467-018-4103-3.

PMID:
30443740
6.

Genetic Testing for Steroid-Resistant-Nephrotic Syndrome in an Outbred Population.

Varner JD, Chryst-Stangl M, Esezobor CI, Solarin A, Wu G, Lane B, Hall G, Abeyagunawardena A, Matory A, Hunley TE, Lin JJ, Howell D, Gbadegesin R.

Front Pediatr. 2018 Oct 22;6:307. doi: 10.3389/fped.2018.00307. eCollection 2018.

7.

Genetic Basis of Health Disparity in Childhood Nephrotic Syndrome.

Varner JD, Matory A, Gbadegesin RA.

Am J Kidney Dis. 2018 Nov;72(5 Suppl 1):S22-S25. doi: 10.1053/j.ajkd.2018.06.022. Review.

PMID:
30343718
8.

Recurrence of nephrotic syndrome following kidney transplantation is associated with initial native kidney biopsy findings.

Pelletier JH, Kumar KR, Engen R, Bensimhon A, Varner JD, Rheault MN, Srivastava T, Straatmann C, Silva C, Davis TK, Wenderfer SE, Gibson K, Selewski D, Barcia J, Weng P, Licht C, Jawa N, Kallash M, Foreman JW, Wigfall DR, Chua AN, Chambers E, Hornik CP, Brewer ED, Nagaraj SK, Greenbaum LA, Gbadegesin RA.

Pediatr Nephrol. 2018 Oct;33(10):1773-1780. doi: 10.1007/s00467-018-3994-3. Epub 2018 Jul 7. Erratum in: Pediatr Nephrol. 2019 Mar;34(3):539.

PMID:
29982878
9.

Sequence Specific Modeling of E. coli Cell-Free Protein Synthesis.

Vilkhovoy M, Horvath N, Shih CH, Wayman JA, Calhoun K, Swartz J, Varner JD.

ACS Synth Biol. 2018 Aug 17;7(8):1844-1857. doi: 10.1021/acssynbio.7b00465. Epub 2018 Jul 16.

PMID:
29944340
10.

Src family kinase inhibitor bosutinib enhances retinoic acid-induced differentiation of HL-60 leukemia cells.

MacDonald RJ, Bunaciu RP, Ip V, Dai D, Tran D, Varner JD, Yen A.

Leuk Lymphoma. 2018 Dec;59(12):2941-2951. doi: 10.1080/10428194.2018.1452213. Epub 2018 Mar 23.

PMID:
29569971
11.

Potential for subsets of wt-NPM1 primary AML blasts to respond to retinoic acid treatment.

Bunaciu RP, MacDonald RJ, Gao F, Johnson LM, Varner JD, Wang X, Nataraj S, Guzman ML, Yen A.

Oncotarget. 2017 Dec 23;9(3):4134-4149. doi: 10.18632/oncotarget.23642. eCollection 2018 Jan 9.

12.

Reduced order modeling and analysis of the human complement system.

Sagar A, Dai W, Minot M, LeCover R, Varner JD.

PLoS One. 2017 Nov 20;12(11):e0187373. doi: 10.1371/journal.pone.0187373. eCollection 2017.

13.

An Effective Model of the Retinoic Acid Induced HL-60 Differentiation Program.

Tasseff R, Jensen HA, Congleton J, Dai D, Rogers KV, Sagar A, Bunaciu RP, Yen A, Varner JD.

Sci Rep. 2017 Oct 30;7(1):14327. doi: 10.1038/s41598-017-14523-5.

14.

JuPOETs: a constrained multiobjective optimization approach to estimate biochemical model ensembles in the Julia programming language.

Bassen DM, Vilkhovoy M, Minot M, Butcher JT, Varner JD.

BMC Syst Biol. 2017 Jan 25;11(1):10. doi: 10.1186/s12918-016-0380-2.

15.

Population Heterogeneity in the Epithelial to Mesenchymal Transition Is Controlled by NFAT and Phosphorylated Sp1.

Gould R, Bassen DM, Chakrabarti A, Varner JD, Butcher J.

PLoS Comput Biol. 2016 Dec 27;12(12):e1005251. doi: 10.1371/journal.pcbi.1005251. eCollection 2016 Dec.

16.

Differential Contributions of Intrinsic and Extrinsic Pathways to Thrombin Generation in Adult, Maternal and Cord Plasma Samples.

Rice NT, Szlam F, Varner JD, Bernstein PS, Szlam AD, Tanaka KA.

PLoS One. 2016 May 19;11(5):e0154127. doi: 10.1371/journal.pone.0154127. eCollection 2016.

17.

Induced myelomonocytic differentiation in leukemia cells is accompanied by noncanonical transcription factor expression.

Jensen HA, Yourish HB, Bunaciu RP, Varner JD, Yen A.

FEBS Open Bio. 2015 Sep 28;5:789-800. doi: 10.1016/j.fob.2015.09.008. eCollection 2015.

18.

6-Formylindolo(3,2-b)Carbazole (FICZ) Modulates the Signalsome Responsible for RA-Induced Differentiation of HL-60 Myeloblastic Leukemia Cells.

Bunaciu RP, Jensen HA, MacDonald RJ, LaTocha DH, Varner JD, Yen A.

PLoS One. 2015 Aug 19;10(8):e0135668. doi: 10.1371/journal.pone.0135668. eCollection 2015.

19.

Generating Effective Models and Parameters for RNA Genetic Circuits.

Hu CY, Varner JD, Lucks JB.

ACS Synth Biol. 2015 Aug 21;4(8):914-26. doi: 10.1021/acssynbio.5b00077. Epub 2015 Jul 2.

20.

GW5074 and PP2 kinase inhibitors implicate nontraditional c-Raf and Lyn function as drivers of retinoic acid-induced maturation.

Jensen HA, Bunaciu RP, Varner JD, Yen A.

Cell Signal. 2015 Aug;27(8):1666-75. doi: 10.1016/j.cellsig.2015.03.014. Epub 2015 Mar 26.

21.

Retinoic acid therapy resistance progresses from unilineage to bilineage in HL-60 leukemic blasts.

Jensen HA, Bunaciu RP, Ibabao CN, Myers R, Varner JD, Yen A.

PLoS One. 2014 Jun 12;9(6):e98929. doi: 10.1371/journal.pone.0098929. eCollection 2014.

22.

Ubiquibodies, synthetic E3 ubiquitin ligases endowed with unnatural substrate specificity for targeted protein silencing.

Portnoff AD, Stephens EA, Varner JD, DeLisa MP.

J Biol Chem. 2014 Mar 14;289(11):7844-55. doi: 10.1074/jbc.M113.544825. Epub 2014 Jan 28.

23.

Physicochemical regulation of endothelial sprouting in a 3D microfluidic angiogenesis model.

Verbridge SS, Chakrabarti A, DelNero P, Kwee B, Varner JD, Stroock AD, Fischbach C.

J Biomed Mater Res A. 2013 Oct;101(10):2948-56. doi: 10.1002/jbm.a.34587. Epub 2013 Apr 5.

24.

The Src-family kinase inhibitor PP2 rescues inducible differentiation events in emergent retinoic acid-resistant myeloblastic leukemia cells.

Jensen HA, Styskal LE, Tasseff R, Bunaciu RP, Congleton J, Varner JD, Yen A.

PLoS One. 2013;8(3):e58621. doi: 10.1371/journal.pone.0058621. Epub 2013 Mar 15.

25.

Hierarchical approaches for systems modeling in cardiac development.

Gould RA, Aboulmouna LM, Varner JD, Butcher JT.

Wiley Interdiscip Rev Syst Biol Med. 2013 May-Jun;5(3):289-305. doi: 10.1002/wsbm.1217. Epub 2013 Mar 5. Review.

26.

Multiscale models of breast cancer progression.

Chakrabarti A, Verbridge S, Stroock AD, Fischbach C, Varner JD.

Ann Biomed Eng. 2012 Nov;40(11):2488-500. doi: 10.1007/s10439-012-0655-8. Epub 2012 Sep 25. Review.

27.

Computational modeling and analysis of insulin induced eukaryotic translation initiation.

Lequieu J, Chakrabarti A, Nayak S, Varner JD.

PLoS Comput Biol. 2011 Nov;7(11):e1002263. doi: 10.1371/journal.pcbi.1002263. Epub 2011 Nov 10.

28.

A review of the mammalian unfolded protein response.

Chakrabarti A, Chen AW, Varner JD.

Biotechnol Bioeng. 2011 Dec;108(12):2777-93. doi: 10.1002/bit.23282. Epub 2011 Aug 9. Review.

29.

Interferon regulatory factor-1 binds c-Cbl, enhances mitogen activated protein kinase signaling and promotes retinoic acid-induced differentiation of HL-60 human myelo-monoblastic leukemia cells.

Shen M, Bunaciu RP, Congleton J, Jensen HA, Sayam LG, Varner JD, Yen A.

Leuk Lymphoma. 2011 Dec;52(12):2372-9. doi: 10.3109/10428194.2011.603449. Epub 2011 Aug 24.

30.

Modeling and analysis of retinoic acid induced differentiation of uncommitted precursor cells.

Tasseff R, Nayak S, Song SO, Yen A, Varner JD.

Integr Biol (Camb). 2011 May;3(5):578-91. doi: 10.1039/c0ib00141d. Epub 2011 Mar 24.

31.

Modelling and analysis of an ensemble of eukaryotic translation initiation models.

Nayak S, Siddiqui JK, Varner JD.

IET Syst Biol. 2011 Jan;5(1):2. doi: 10.1049/iet-syb.2009.0065.

PMID:
21261397
32.

Ensembles of uncertain mathematical models can identify network response to therapeutic interventions.

Luan D, Szlam F, Tanaka KA, Barie PS, Varner JD.

Mol Biosyst. 2010 Nov;6(11):2272-86. doi: 10.1039/b920693k. Epub 2010 Sep 16.

PMID:
20844798
33.

RAF associates with phosphorylated nuclear BubR1 during endoreduplication induced by JAK inhibition.

Reiterer G, Chen L, Tassef R, Varner JD, Chen CY, Yen A.

Cell Cycle. 2010 Aug 15;9(16):3297-304. doi: 10.4161/cc.9.16.12631. Epub 2010 Aug 10.

34.

Ensembles of signal transduction models using Pareto Optimal Ensemble Techniques (POETs).

Song SO, Chakrabarti A, Varner JD.

Biotechnol J. 2010 Jul;5(7):768-80. doi: 10.1002/biot.201000059.

35.
36.

Analysis of the molecular networks in androgen dependent and independent prostate cancer revealed fragile and robust subsystems.

Tasseff R, Nayak S, Salim S, Kaushik P, Rizvi N, Varner JD.

PLoS One. 2010 Jan 28;5(1):e8864. doi: 10.1371/journal.pone.0008864.

37.

Anti-factor IXa Aptamer reduces propagation of thrombin generation in plasma anticoagulated with warfarin.

Szlam F, Luan D, Bolliger D, Szlam AD, Levy JH, Varner JD, Tanaka KA.

Thromb Res. 2010 May;125(5):432-7. doi: 10.1016/j.thromres.2009.11.018. Epub 2009 Dec 11.

PMID:
20004955
38.

A hybrid model of anaerobic E. coli GJT001: combination of elementary flux modes and cybernetic variables.

Kim JI, Varner JD, Ramkrishna D.

Biotechnol Prog. 2008 Sep-Oct;24(5):993-1006. doi: 10.1002/btpr.73.

PMID:
19194908
39.

Engineering the spatial organization of metabolic enzymes: mimicking nature's synergy.

Conrado RJ, Varner JD, DeLisa MP.

Curr Opin Biotechnol. 2008 Oct;19(5):492-9. doi: 10.1016/j.copbio.2008.07.006. Epub 2008 Sep 6. Review.

PMID:
18725290
40.

A test of highly optimized tolerance reveals fragile cell-cycle mechanisms are molecular targets in clinical cancer trials.

Nayak S, Salim S, Luan D, Zai M, Varner JD.

PLoS One. 2008 Apr 23;3(4):e2016. doi: 10.1371/journal.pone.0002016.

41.
42.

Stochastic reaction-diffusion simulation of enzyme compartmentalization reveals improved catalytic efficiency for a synthetic metabolic pathway.

Conrado RJ, Mansell TJ, Varner JD, DeLisa MP.

Metab Eng. 2007 Jul;9(4):355-63. Epub 2007 May 26.

PMID:
17601761
43.
44.

Cybernetic model predictive control of a continuous bioreactor with cell recycle.

Gadkar KG, Doyle FJ 3rd, Crowley TJ, Varner JD.

Biotechnol Prog. 2003 Sep-Oct;19(5):1487-97.

PMID:
14524710
45.

Large-scale prediction of phenotype: concept.

Varner JD.

Biotechnol Bioeng. 2000 Sep 20;69(6):664-78.

PMID:
10918142

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