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Items: 1 to 50 of 64

1.

Revised Formulation of Fick's, Fourier's, and Newton's Laws for Spatially Varying Linear Transport Coefficients.

Won YY, Ramkrishna D.

ACS Omega. 2019 Jun 27;4(6):11215-11222. doi: 10.1021/acsomega.9b00736. eCollection 2019 Jun 30.

2.

Consistency of cybernetic variables with gene expression profiles: A more rigorous test.

DeVilbiss F, Mandli A, Ramkrishna D.

Biotechnol Prog. 2018 Jul;34(4):858-867. doi: 10.1002/btpr.2654. Epub 2018 Jul 1.

PMID:
29708637
3.

Insulin exits skeletal muscle capillaries by fluid-phase transport.

Williams IM, Valenzuela FA, Kahl SD, Ramkrishna D, Mezo AR, Young JD, Wells KS, Wasserman DH.

J Clin Invest. 2018 Feb 1;128(2):699-714. doi: 10.1172/JCI94053. Epub 2018 Jan 8.

4.

Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming.

Song HS, Goldberg N, Mahajan A, Ramkrishna D.

Bioinformatics. 2017 Aug 1;33(15):2345-2353. doi: 10.1093/bioinformatics/btx171.

PMID:
28369193
5.

Nanocrystal Dissolution Kinetics and Solubility Increase Prediction from Molecular Dynamics: The Case of α-, β-, and γ-Glycine.

Parks C, Koswara A, Tung HH, Nere NK, Bordawekar S, Nagy ZK, Ramkrishna D.

Mol Pharm. 2017 Apr 3;14(4):1023-1032. doi: 10.1021/acs.molpharmaceut.6b00882. Epub 2017 Mar 8.

PMID:
28271901
6.

Solubility curves and nucleation rates from molecular dynamics for polymorph prediction - moving beyond lattice energy minimization.

Parks C, Koswara A, DeVilbiss F, Tung HH, Nere NK, Bordawekar S, Nagy ZK, Ramkrishna D.

Phys Chem Chem Phys. 2017 Feb 15;19(7):5285-5295. doi: 10.1039/c6cp07181c.

PMID:
28149994
7.

Comment on "Mathematical modeling of unicellular microalgae and cyanobacteria metabolism for biofuel production" by Baroukh et al. [Curr Opin Biotechnol. 2015, 33:198-205].

Song HS, Ramkrishna D.

Curr Opin Biotechnol. 2016 Apr;38:198-9. doi: 10.1016/j.copbio.2016.02.026. Epub 2016 Mar 16. No abstract available.

PMID:
26994667
8.

On speeding up stochastic simulations by parallelization of random number generation.

Shu CC, Tran V, Binagia J, Ramkrishna D.

Chem Eng Sci. 2015 Dec 1;137:828-836.

9.

Model-Based Individualized Treatment of Chemotherapeutics: Bayesian Population Modeling and Dose Optimization.

Jayachandran D, Laínez-Aguirre J, Rundell A, Vik T, Hannemann R, Reklaitis G, Ramkrishna D.

PLoS One. 2015 Jul 30;10(7):e0133244. doi: 10.1371/journal.pone.0133244. eCollection 2015.

10.

Engineering surface hydrophobicity improves activity of Bacillus thermocatenulatus lipase 2 enzyme.

Tang T, Yuan C, Hwang HT, Zhao X, Ramkrishna D, Liu D, Varma A.

Biotechnol J. 2015 Sep;10(11):1762-9. doi: 10.1002/biot.201500011. Epub 2015 Jul 16.

PMID:
26097135
11.

New "Tau-Leap" Strategy for Accelerated Stochastic Simulation.

Ramkrishna D, Shu CC, Tran V.

Ind Eng Chem Res. 2014 Dec 10;53(49):18975-18981. Epub 2014 Sep 22.

12.

Optimal chemotherapy for leukemia: a model-based strategy for individualized treatment.

Jayachandran D, Rundell AE, Hannemann RE, Vik TA, Ramkrishna D.

PLoS One. 2014 Oct 13;9(10):e109623. doi: 10.1371/journal.pone.0109623. eCollection 2014.

13.

Revitalizing personalized medicine: respecting biomolecular complexities beyond gene expression.

Jayachandran D, Ramkrishna U, Skiles J, Renbarger J, Ramkrishna D.

CPT Pharmacometrics Syst Pharmacol. 2014 Apr 16;3:e110. doi: 10.1038/psp.2014.6.

14.

Population balance modeling: current status and future prospects.

Ramkrishna D, Singh MR.

Annu Rev Chem Biomol Eng. 2014;5:123-46. doi: 10.1146/annurev-chembioeng-060713-040241. Epub 2014 Mar 3. Review.

PMID:
24606333
15.

Lipase-catalyzed process for biodiesel production: protein engineering and lipase production.

Hwang HT, Qi F, Yuan C, Zhao X, Ramkrishna D, Liu D, Varma A.

Biotechnol Bioeng. 2014 Apr;111(4):639-53. doi: 10.1002/bit.25162. Epub 2013 Dec 17. Review.

PMID:
24284881
16.

Role of intracellular stochasticity in biofilm growth. Insights from population balance modeling.

Shu CC, Chatterjee A, Hu WS, Ramkrishna D.

PLoS One. 2013 Nov 13;8(11):e79196. doi: 10.1371/journal.pone.0079196. eCollection 2013.

17.

Antagonistic self-sensing and mate-sensing signaling controls antibiotic-resistance transfer.

Chatterjee A, Cook LC, Shu CC, Chen Y, Manias DA, Ramkrishna D, Dunny GM, Hu WS.

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):7086-90. doi: 10.1073/pnas.1212256110. Epub 2013 Apr 8.

18.

Dynamic modeling of aerobic growth of Shewanella oneidensis. Predicting triauxic growth, flux distributions, and energy requirement for growth.

Song HS, Ramkrishna D, Pinchuk GE, Beliaev AS, Konopka AE, Fredrickson JK.

Metab Eng. 2013 Jan;15:25-33. doi: 10.1016/j.ymben.2012.08.004. Epub 2012 Sep 26.

PMID:
23022551
19.

Exacting predictions by cybernetic model confirmed experimentally: steady state multiplicity in the chemostat.

Kim JI, Song HS, Sunkara SR, Lali A, Ramkrishna D.

Biotechnol Prog. 2012 Sep-Oct;28(5):1160-6. doi: 10.1002/btpr.1583. Epub 2012 Jul 16.

PMID:
22736577
20.

MODELING OF GENE REGULATORY PROCESSES BY POPULATION MEDIATED SIGNALING. NEW APPLICATIONS OF POPULATION BALANCES.

Shu CC, Chatterjee A, Hu WS, Ramkrishna D.

Chem Eng Sci. 2012 Mar 5;70:188-199. Epub 2011 Aug 11.

21.

Prediction of dynamic behavior of mutant strains from limited wild-type data.

Song HS, Ramkrishna D.

Metab Eng. 2012 Mar;14(2):69-80.

PMID:
22500302
22.

Prediction of dynamic metabolic behavior of Pediococcus pentosaceus producing lactic acid from lignocellulosic sugars.

Adler P, Song HS, Kästner K, Ramkrishna D, Kunz B.

Biotechnol Prog. 2012 May-Jun;28(3):623-35. doi: 10.1002/btpr.1521. Epub 2012 Feb 9.

PMID:
22275308
23.

On enhancing productivity of bioethanol with multiple species.

Geng J, Song HS, Yuan J, Ramkrishna D.

Biotechnol Bioeng. 2012 Jun;109(6):1508-17. doi: 10.1002/bit.24419. Epub 2012 Jan 7.

PMID:
22234672
24.

Bistability versus bimodal distributions in gene regulatory processes from population balance.

Shu CC, Chatterjee A, Dunny G, Hu WS, Ramkrishna D.

PLoS Comput Biol. 2011 Aug;7(8):e1002140. doi: 10.1371/journal.pcbi.1002140. Epub 2011 Aug 25. Erratum in: PLoS Comput Biol. 2011 Oct;7(10). doi: 10.1371/annotation/9c1b51d2-1957-43ff-81bc-da833eda0b8c.

25.

Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation.

Chatterjee A, Johnson CM, Shu CC, Kaznessis YN, Ramkrishna D, Dunny GM, Hu WS.

Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9721-6. doi: 10.1073/pnas.1101569108. Epub 2011 May 23.

26.

Cybernetic models based on lumped elementary modes accurately predict strain-specific metabolic function.

Song HS, Ramkrishna D.

Biotechnol Bioeng. 2011 Jan;108(1):127-40. doi: 10.1002/bit.22922.

PMID:
20830732
27.

Prediction of metabolic function from limited data: Lumped hybrid cybernetic modeling (L-HCM).

Song HS, Ramkrishna D.

Biotechnol Bioeng. 2010 Jun 1;106(2):271-84. doi: 10.1002/bit.22692.

PMID:
20148411
28.

Using adaptive model predictive control to customize maintenance therapy chemotherapeutic dosing for childhood acute lymphoblastic leukemia.

Noble SL, Sherer E, Hannemann RE, Ramkrishna D, Vik T, Rundell AE.

J Theor Biol. 2010 Jun 7;264(3):990-1002. doi: 10.1016/j.jtbi.2010.01.031. Epub 2010 Feb 4.

PMID:
20138060
29.

Systematic development of hybrid cybernetic models: application to recombinant yeast co-consuming glucose and xylose.

Song HS, Morgan JA, Ramkrishna D.

Biotechnol Bioeng. 2009 Aug 1;103(5):984-1002. doi: 10.1002/bit.22332.

PMID:
19449391
30.

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
31.

Reduction of a set of elementary modes using yield analysis.

Song HS, Ramkrishna D.

Biotechnol Bioeng. 2009 Feb 1;102(2):554-68. doi: 10.1002/bit.22062.

PMID:
18853408
32.

New patterns of mixed-substrate utilization during batch growth of Escherichia coli K12.

Narang A, Konopka A, Ramkrishna D.

Biotechnol Bioeng. 1997 Sep 5;55(5):747-57. doi: 10.1002/(SICI)1097-0290(19970905)55:5<747::AID-BIT5>3.0.CO;2-B.

PMID:
18636585
33.

Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control.

Young JD, Henne KL, Morgan JA, Konopka AE, Ramkrishna D.

Biotechnol Bioeng. 2008 Jun 15;100(3):542-59. doi: 10.1002/bit.21780.

PMID:
18438875
34.

Solving the inverse problem for aggregation in activated sludge flocculation using a population balance framework.

Nopens I, Nere N, Vanrolleghem PA, Ramkrishna D.

Water Sci Technol. 2007;56(6):95-103.

PMID:
17898448
35.

Identification of age-structured models: cell cycle phase transitions.

Sherer E, Tocce E, Hannemann RE, Rundell AE, Ramkrishna D.

Biotechnol Bioeng. 2008 Mar 1;99(4):960-74.

PMID:
17787014
36.

Estimation of likely cancer cure using first- and second-order product densities of population balance models.

Sherer E, Hannemann RE, Rundell A, Ramkrishna D.

Ann Biomed Eng. 2007 Jun;35(6):903-15. Epub 2007 Apr 14.

PMID:
17440813
37.

On the matching and proportional laws of cybernetic models.

Young JD, Ramkrishna D.

Biotechnol Prog. 2007 Jan-Feb;23(1):83-99.

PMID:
17269675
38.

Analysis of resonance chemotherapy in leukemia treatment via multi-staged population balance models.

Sherer E, Hannemann RE, Rundell A, Ramkrishna D.

J Theor Biol. 2006 Jun 21;240(4):648-61. Epub 2006 Jan 23.

PMID:
16430925
39.

Unveiling steady-state multiplicity in hybridoma cultures: the cybernetic approach.

Namjoshi AA, Hu WS, Ramkrishna D.

Biotechnol Bioeng. 2003 Jan 5;81(1):80-91.

PMID:
12432584
40.

Cybernetic modeling and regulation of metabolic pathways in multiple steady states of hybridoma cells.

Guardia MJ, Gambhir A, Europa AF, Ramkrishna D, Hu WS.

Biotechnol Prog. 2000 Sep-Oct;16(5):847-53.

PMID:
11027180
41.

Metabolic engineering from a cybernetic perspective: aspartate family of amino acids.

Varner J, Ramkrishna D.

Metab Eng. 1999 Jan;1(1):88-116.

PMID:
10935757
43.

Metabolic engineering from a cybernetic perspective. 1. Theoretical preliminaries

Varner J, Ramkrishna D.

Biotechnol Prog. 1999 May;15(3):407-25.

PMID:
10356258
44.

Mathematical models of metabolic pathways.

Varner J, Ramkrishna D.

Curr Opin Biotechnol. 1999 Apr;10(2):146-50. Review.

PMID:
10209144
45.

Application of cybernetic models to metabolic engineering: investigation of storage pathways

Varner J, Ramkrishna D.

Biotechnol Bioeng. 1998 Apr 5;58(2-3):282-91.

PMID:
10191402
46.

Microbial growth on substitutable substrates: characterizing the consumer-resource relationship.

Ramakrishna R, Ramkrishna D, Konopka AE.

Biotechnol Bioeng. 1997 Apr 5;54(1):77-90.

PMID:
18634075
47.

The Dynamics of Microbial Growth on Mixtures of Substrates in Batch Reactors.

Narang A, Konopka A, Ramkrishna D.

J Theor Biol. 1997 Feb 7;184(3):301-317. doi: 10.1006/jtbi.1996.0275.

PMID:
31940741
48.

Cybernetic modeling of growth in mixed, substitutable substrate environments: Preferential and simultaneous utilization.

Ramakrishna R, Ramkrishna D, Konopka AE.

Biotechnol Bioeng. 1996 Oct 5;52(1):141-51.

PMID:
18629860
49.

Toward a self-similar theory of microbial populations.

Ramkrishna D.

Biotechnol Bioeng. 1994 Jan 20;43(2):138-48.

PMID:
18615607
50.

Upper critical dimension for aggregation processes.

Wright H, Ramkrishna D.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1993 May;47(5):3225-3230. No abstract available.

PMID:
9960374

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