Shankar Subramaniam

Shankar Subramaniam

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Shankar Subramaniam

Publications by authors named "Shankar Subramaniam"

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Attractor Ranked Radial Basis Function Network: A Nonparametric Forecasting Approach for Chaotic Dynamic Systems.

Sci Rep 2020 Mar 2;10(1):3780. Epub 2020 Mar 2.

University of California San Diego, Departments of Bioengineering and Computer Science & Engineering, La Jolla, CA, 92093, USA.

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http://dx.doi.org/10.1038/s41598-020-60606-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7052196PMC
March 2020

Skeletal muscle: A review of molecular structure and function, in health and disease.

Wiley Interdiscip Rev Syst Biol Med 2020 Jan 13;12(1):e1462. Epub 2019 Aug 13.

Department of Bioengineering, Bioinformatics & Systems Biology, University of California, San Diego, California.

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http://dx.doi.org/10.1002/wsbm.1462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6916202PMC
January 2020

Co-Expression Network Approach to Studying the Effects of Botulinum Neurotoxin-A.

IEEE/ACM Trans Comput Biol Bioinform 2018 Nov-Dec;15(6):2009-2016. Epub 2017 Oct 17.

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http://dx.doi.org/10.1109/TCBB.2017.2763949DOI Listing
July 2019

Time varying causal network reconstruction of a mouse cell cycle.

BMC Bioinformatics 2019 May 29;20(1):294. Epub 2019 May 29.

Department of Bioengineering, Departments of Computer Science and Engineering, Cellular and Molecular Medicine, and the Graduate Program in Bioinformatics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.

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http://dx.doi.org/10.1186/s12859-019-2895-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6542064PMC
May 2019

Topological and functional comparison of community detection algorithms in biological networks.

BMC Bioinformatics 2019 Apr 27;20(1):212. Epub 2019 Apr 27.

Department of Bioengineering, Departments of Computer Science and Engineering, Cellular and Molecular Medicine, and the Graduate Program in Bioinformatics, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.

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http://dx.doi.org/10.1186/s12859-019-2746-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6487005PMC
April 2019

LIPID MAPS: Serving the next generation of lipid researchers with tools, resources, data, and training.

Sci Signal 2019 01 8;12(563). Epub 2019 Jan 8.

Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1126/scisignal.aaw2964DOI Listing
January 2019

Evaluation of vibrant muscles over the shoulder region among workers of the hand screen printing industry.

Int J Occup Saf Ergon 2018 Jun 2;24(2):278-285. Epub 2017 Mar 2.

a Department of Mechatronics Engineering , Kongu Engineering College , India.

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http://dx.doi.org/10.1080/10803548.2017.1280914DOI Listing
June 2018

Rheological transition in simple shear of moderately dense assemblies of dry cohesive granules.

Phys Rev E 2018 Jun;97(6-1):062902

Center for Multiphase Flow Research and Education, Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011, USA.

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http://dx.doi.org/10.1103/PhysRevE.97.062902DOI Listing
June 2018

miRNAs that Induce Human Cardiomyocyte Proliferation Converge on the Hippo Pathway.

Cell Rep 2018 05;23(7):2168-2174

Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Stanford Cardiovascular Institute and Department of Medicine, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.04.049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6261450PMC
May 2018

Assessment of shoulder and low back muscle activity of male kitchen workers using surface electromyography.

Int J Occup Med Environ Health 2018 01 20;31(1):81-90. Epub 2017 Sep 20.

University of Quebec, Montreal, Quebec, Canada (National Institute of Scientific Research, Energy Materials Telecommunications Research Centre).

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http://dx.doi.org/10.13075/ijomeh.1896.00903DOI Listing
January 2018

Co-expression Network Approach Reveals Functional Similarities among Diseases Affecting Human Skeletal Muscle.

Front Physiol 2017 1;8:980. Epub 2017 Dec 1.

Departments Cellular and Molecular Medicine, Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States.

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http://dx.doi.org/10.3389/fphys.2017.00980DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5717538PMC
December 2017

Community Structure Analysis of Gene Interaction Networks in Duchenne Muscular Dystrophy.

PLoS One 2013 19;8(6):e67237. Epub 2013 Jun 19.

Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067237PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3686745PMC
October 2017

Krüppel-Like Factor 4 Regulation of Cholesterol-25-Hydroxylase and Liver X Receptor Mitigates Atherosclerosis Susceptibility.

Circulation 2017 Oct 9;136(14):1315-1330. Epub 2017 Aug 9.

From Cardiovascular Research Center, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, China (Z.L., Jin Zhang, L.B., Jiao Zhang, M.H., J.L., T.L., J.Y.-J.S.); Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education of China (Z.L., Jin Zhang, L.B., Jiao Zhang, M.H., J.L., T.L., J.Y.-J.S.); Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla (M.M., Jin Zhang, J.K., M.H., Y.-J.X., M.J., J.Y.-J.S.);Department of Bioengineering, University of California, San Diego, La Jolla (M.R.M., S.G.); Division of Biochemistry and Molecular Biology, University of California, Riverside (M.M.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (H.-Y.H., H.-D.H.); and Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH (G.Z., P.S., M.K.J.).

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http://dx.doi.org/10.1161/CIRCULATIONAHA.117.027462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5741092PMC
October 2017

Systems biology analysis of longitudinal functional response of endothelial cells to shear stress.

Proc Natl Acad Sci U S A 2017 10 26;114(41):10990-10995. Epub 2017 Sep 26.

Bioinformatics and Systems Biology Graduate Program, University of California at San Diego, La Jolla, CA 92023;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1707517114
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http://dx.doi.org/10.1073/pnas.1707517114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5642700PMC
October 2017

LINC00341 exerts an anti-inflammatory effect on endothelial cells by repressing VCAM1.

Physiol Genomics 2017 Jul 12;49(7):339-345. Epub 2017 May 12.

Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California;

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http://dx.doi.org/10.1152/physiolgenomics.00132.2016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538877PMC
July 2017

Epigenetic Regulation: A New Frontier for Biomedical Engineers.

Annu Rev Biomed Eng 2017 06 6;19:195-219. Epub 2017 Mar 6.

Department of Medicine, University of California at San Diego, La Jolla, California 92093; email: ,

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http://dx.doi.org/10.1146/annurev-bioeng-071516-044720DOI Listing
June 2017

Metabolic Phenotypes of Response to Vaccination in Humans.

Cell 2017 May 11;169(5):862-877.e17. Epub 2017 May 11.

Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road, Atlanta, GA 30329, USA; Department of Pathology, School of Medicine, Emory University, Atlanta, GA 30329, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.04.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711477PMC
May 2017

A benign alternative process for efficient separation of pure commercially important flavonoid nutraceuticals from edible plants.

J Food Sci Technol 2017 May 22;54(6):1519-1526. Epub 2017 Mar 22.

School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613402 India.

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http://dx.doi.org/10.1007/s13197-017-2583-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5430184PMC
May 2017

Three distinct cell populations express extracellular matrix proteins and increase in number during skeletal muscle fibrosis.

Am J Physiol Cell Physiol 2017 Feb 23;312(2):C131-C143. Epub 2016 Nov 23.

Department of Bioengineering, University of California San Diego, La Jolla, California;

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http://dx.doi.org/10.1152/ajpcell.00226.2016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5336596PMC
February 2017

Loss of EGFR-ASAP1 signaling in metastatic and unresectable hepatoblastoma.

Sci Rep 2016 12 2;6:38347. Epub 2016 Dec 2.

Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, 4401 Penn Avenue, Pediatric Abdominal Transplant Surgery, Pittsburgh, PA 15224, USA.

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http://dx.doi.org/10.1038/srep38347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133573PMC
December 2016

p62/SQSTM1 by Binding to Vitamin D Receptor Inhibits Hepatic Stellate Cell Activity, Fibrosis, and Liver Cancer.

Cancer Cell 2016 10;30(4):595-609

Cancer Metabolism and Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5081228PMC
http://dx.doi.org/10.1016/j.ccell.2016.09.004DOI Listing
October 2016

Serum microRNAs explain discordance of non-alcoholic fatty liver disease in monozygotic and dizygotic twins: a prospective study.

Gut 2016 09 22;65(9):1546-54. Epub 2015 May 22.

NAFLD Translational Research Unit, University of California, San Diego, La Jolla, California, USA Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California, USA Division of Epidemiology, Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, California, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5089367PMC
http://dx.doi.org/10.1136/gutjnl-2015-309456DOI Listing
September 2016

Systems Analysis of the Complement-Induced Priming Phase of Liver Regeneration.

J Immunol 2016 09 10;197(6):2500-8. Epub 2016 Aug 10.

Graduate Program in Bioinformatics, Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093; Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093; Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093; and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093

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http://dx.doi.org/10.4049/jimmunol.1600628DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5038987PMC
September 2016

Computational Modeling of Competitive Metabolism between ω3- and ω6-Polyunsaturated Fatty Acids in Inflammatory Macrophages.

J Phys Chem B 2016 08 26;120(33):8346-53. Epub 2016 Apr 26.

Department of Bioengineering and San Diego Supercomputer Center, University of California at San Diego , 9500 Gilman Drive, La Jolla, California 92093-0412, United States.

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http://dx.doi.org/10.1021/acs.jpcb.6b02036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5024554PMC
August 2016

p62, Upregulated during Preneoplasia, Induces Hepatocellular Carcinogenesis by Maintaining Survival of Stressed HCC-Initiating Cells.

Cancer Cell 2016 06 19;29(6):935-948. Epub 2016 May 19.

Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Pathology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2016.04.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907799PMC
June 2016

The Role of ARF6 in Biliary Atresia.

PLoS One 2015 17;10(9):e0138381. Epub 2015 Sep 17.

Hillman Center for Pediatric Transplantation of the Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, 15224, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0138381PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574480PMC
May 2016

Anti-neutrophil cytoplasmic antibody negative crescentic paucimmune glomerulonephritis in a case of scleroderma with systemic lupus erythematosus overlap.

Saudi J Kidney Dis Transpl 2016 May;27(3):602-5

Department of Pathology, Armed Forces Medical College, Pune, Maharashtra, India.

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http://dx.doi.org/10.4103/1319-2442.182439DOI Listing
May 2016

Investigation of work-related musculoskeletal disorders among male kitchen workers in South India.

Int J Occup Saf Ergon 2015 ;21(4):524-31

a Kongu Engineering College , India.

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http://dx.doi.org/10.1080/10803548.2015.1096063DOI Listing
March 2016

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools.

Nucleic Acids Res 2016 Jan 13;44(D1):D463-70. Epub 2015 Oct 13.

San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA Departments of Bioengineering, Computer Science and Engineering, Cellular and Molecular Medicine, and Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA

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http://dx.doi.org/10.1093/nar/gkv1042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702780PMC
January 2016

Systems Analysis of Immunity to Influenza Vaccination across Multiple Years and in Diverse Populations Reveals Shared Molecular Signatures.

Immunity 2015 Dec;43(6):1186-98

Department of Pathology, School of Medicine, Emory University, 1648 Pierce Drive NE, Atlanta, GA 30307, USA; Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road, Atlanta, GA 30329, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2015.11.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4859820PMC
December 2015

Scope and limitations of yeast as a model organism for studying human tissue-specific pathways.

BMC Syst Biol 2015 Dec 29;9:96. Epub 2015 Dec 29.

Department of Computer Sciences, Purdue University, West Lafayette, 47907, USA.

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http://www.biomedcentral.com/1752-0509/9/96
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http://dx.doi.org/10.1186/s12918-015-0253-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4696342PMC
December 2015

Systems vaccinology: Enabling rational vaccine design with systems biological approaches.

Vaccine 2015 Sep 6;33(40):5294-301. Epub 2015 Apr 6.

Department of Pathology, Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road, Atlanta, GA 30329, USA; Yerkes National Primate Research Center, Atlanta, GA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.vaccine.2015.03.072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581890PMC
September 2015

Dysregulated mechanisms underlying Duchenne muscular dystrophy from co-expression network preservation analysis.

BMC Res Notes 2015 May 3;8:182. Epub 2015 May 3.

Bioinformatics and System Biology Graduate Program, University of California San Diego, 9500 Gilman Drive, MC0412, La Jolla, CA, 92093, USA.

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http://dx.doi.org/10.1186/s13104-015-1141-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424514PMC
May 2015

Development and extraction optimization of baicalein and pinostrobin from Scutellaria violacea through response surface methodology.

Pharmacogn Mag 2015 May;11(Suppl 1):S127-38

Department of Chemistry, School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India.

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http://dx.doi.org/10.4103/0973-1296.157714DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461952PMC
May 2015

Wnt pathway activation increases hypoxia tolerance during development.

PLoS One 2014 5;9(8):e103292. Epub 2014 Aug 5.

Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America; Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America; Departments of Cellular and Molecular Medicine, Chemistry and Biochemistry and Nanoengineering, University of California San Diego, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0103292PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4122365PMC
April 2015

Drug discovery and the maze of biological complexity: an editorial essay.

Wiley Interdiscip Rev Syst Biol Med 2014 May-Jun;6(3):225-6. Epub 2014 Mar 19.

Departments of Bioengineering, Chemistry and Biochemistry, Cellular and Molecular Medicine, and Nano Engineering, University of California, San Diego, San Diego, CA, USA.

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http://dx.doi.org/10.1002/wsbm.1266DOI Listing
December 2014

Systems analysis of transcriptional data provides insights into muscle's biological response to botulinum toxin.

Muscle Nerve 2014 Nov 17;50(5):744-58. Epub 2014 Mar 17.

Bioinformatics and System Biology Graduate Program, University of California San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1002/mus.24211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136975PMC
November 2014

Influence of serological factors and BMI on the blood pressure/hematocrit association in healthy young men and women.

Vasc Health Risk Manag 2014 6;10:271-7. Epub 2014 May 6.

Department of Experimental Medicine, Faculty of Medicine, Universidad Nacional Autónoma de México, Hospital General de México Dr Eduardo Liceaga, México City, Mexico.

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http://dx.doi.org/10.2147/VHRM.S60130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018417PMC
September 2014

Statistical insights into major human muscular diseases.

Hum Mol Genet 2014 Jul 25;23(14):3772-8. Epub 2014 Feb 25.

Department of Bioengineering, Department of Cellular and Molecular Medicine and Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA

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http://dx.doi.org/10.1093/hmg/ddu090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4415066PMC
July 2014

MicroRNA-23b regulates cyclin-dependent kinase-activating kinase complex through cyclin H repression to modulate endothelial transcription and growth under flow.

Arterioscler Thromb Vasc Biol 2014 Jul 22;34(7):1437-45. Epub 2014 May 22.

From the Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla.

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http://dx.doi.org/10.1161/ATVBAHA.114.303473DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119726PMC
July 2014

Information theoretic approach to complex biological network reconstruction: application to cytokine release in RAW 264.7 macrophages.

BMC Syst Biol 2014 Jun 25;8:77. Epub 2014 Jun 25.

Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, 92093-0412 La Jolla, CA, USA.

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http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
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http://dx.doi.org/10.1186/1752-0509-8-77DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4094931PMC
June 2014

Characterization of sheared colloidal aggregation using Langevin dynamics simulation.

Phys Rev E Stat Nonlin Soft Matter Phys 2014 Jun 25;89(6):062312. Epub 2014 Jun 25.

Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011, USA.

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http://dx.doi.org/10.1103/PhysRevE.89.062312DOI Listing
June 2014

Quantitative transcriptomics using designed primer-based amplification.

Sci Rep 2013 ;3:1740

Bioinformatics and Systems Biology Graduate Program, University of California at San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/srep01740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3638165PMC
February 2014

Modeling of eicosanoid fluxes reveals functional coupling between cyclooxygenases and terminal synthases.

Biophys J 2014 Feb;106(4):966-75

Department of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California at San Diego, La Jolla, California; Department of Bioengineering, University of California at San Diego, La Jolla, California; Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00063495140008
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http://dx.doi.org/10.1016/j.bpj.2014.01.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3945033PMC
February 2014

A Newtonian framework for community detection in undirected biological networks.

IEEE Trans Biomed Circuits Syst 2014 Feb;8(1):65-73

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http://dx.doi.org/10.1109/TBCAS.2013.2288155DOI Listing
February 2014

Synergistic antimicrobial profiling of violacein with commercial antibiotics against pathogenic micro-organisms.

Pharm Biol 2014 Jan 30;52(1):86-90. Epub 2013 Sep 30.

Department of Chemistry, School of Chemical and Biotechnology, Sastra University , Thanjavur , India.

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http://www.tandfonline.com/doi/full/10.3109/13880209.2013.81
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http://dx.doi.org/10.3109/13880209.2013.815634DOI Listing
January 2014

Technical variations in low-input RNA-seq methodologies.

Sci Rep 2014 Jan 14;4:3678. Epub 2014 Jan 14.

1] Bioinformatics and Systems Biology Graduate Program, University of California at San Diego, La Jolla, California, USA [2] Department of Bioengineering, University of California at San Diego, La Jolla, California, USA [3] Departments of Cellular and Molecular Medicine and Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1038/srep03678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890974PMC
January 2014

A combined omics study on activated macrophages--enhanced role of STATs in apoptosis, immunity and lipid metabolism.

Bioinformatics 2013 Nov 26;29(21):2735-43. Epub 2013 Aug 26.

Department of Bioengineering, San Diego Super Computer Center, Department of Cellular and Molecular Medicine and Department of Chemistry and Biochemistry, University of California San Diego, CA 92093, USA.

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http://bioinformatics.oxfordjournals.org/content/early/2013/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btt469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799469PMC
November 2013

Mechanosensitive microRNAs-role in endothelial responses to shear stress and redox state.

Free Radic Biol Med 2013 Sep 30;64:61-8. Epub 2013 May 30.

Biomedical Sciences, School of Medicine, University of California at Riverside, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1016/j.freeradbiomed.2013.05.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762952PMC
September 2013

Developing microRNA screening as a functional genomics tool for disease research.

Front Physiol 2013 27;4:223. Epub 2013 Aug 27.

Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA ; Muscle Development and Regeneration Program, Sanford-Burnham Medical Research Institute La Jolla, CA, USA.

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http://dx.doi.org/10.3389/fphys.2013.00223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753477PMC
August 2013

Inferring the effective TOR-dependent network: a computational study in yeast.

BMC Syst Biol 2013 Aug 30;7:84. Epub 2013 Aug 30.

Department of Computer Science, Purdue University, West Lafayette, Indiana, USA.

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http://dx.doi.org/10.1186/1752-0509-7-84DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016608PMC
August 2013

CMAP: Complement Map Database.

Bioinformatics 2013 Jul 9;29(14):1832-3. Epub 2013 May 9.

Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3702248PMC
July 2013

The poor performance of TMM on microRNA-Seq.

RNA 2013 Jun 24;19(6):735-6. Epub 2013 Apr 24.

Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813, USA.

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http://dx.doi.org/10.1261/rna.039271.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683907PMC
June 2013

Transcriptional abnormalities of hamstring muscle contractures in children with cerebral palsy.

PLoS One 2012 16;7(8):e40686. Epub 2012 Aug 16.

Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431909PMC
January 2013

Functional classification of skeletal muscle networks. II. Applications to pathophysiology.

J Appl Physiol (1985) 2012 Dec 18;113(12):1902-20. Epub 2012 Oct 18.

Department of Bioengineering, University of California San Diego, La Jolla, California 92093-0412, USA.

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http://dx.doi.org/10.1152/japplphysiol.01515.2011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3544493PMC
December 2012

Functional classification of skeletal muscle networks. I. Normal physiology.

J Appl Physiol (1985) 2012 Dec 18;113(12):1884-901. Epub 2012 Oct 18.

Department of Bioengineering, University of California San Diego, La Jolla, CA92093-0412, USA.

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http://dx.doi.org/10.1152/japplphysiol.01514.2011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3544495PMC
December 2012

Stochastic operator-splitting method for reaction-diffusion systems.

J Chem Phys 2012 Nov;137(18):184102

Department of Mechanical and Aerospace Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0411, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3505198PMC
November 2012

Template-based combinatorial enumeration of virtual compound libraries for lipids.

J Cheminform 2012 Sep 25;4(1):23. Epub 2012 Sep 25.

San Diego Supercomputer Center, University of California San Diego, 9500, Gilman Drive, La Jolla, CA 92032, USA.

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http://dx.doi.org/10.1186/1758-2946-4-23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545849PMC
September 2012

Evolution of bioengineering at UCSD: opening new vistas.

IEEE Pulse 2012 Jul;3(4):49-55

Department of Bioengineering, UCSD, San Diego, USA.

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http://dx.doi.org/10.1109/MPUL.2012.2198739DOI Listing
July 2012

Evaluation of normalization methods in mammalian microRNA-Seq data.

RNA 2012 Jun 24;18(6):1279-88. Epub 2012 Apr 24.

Department of Bioengineering, Jacobs School of Engineering, University of California at San Diego, La Jolla, California 92093-0412, USA.

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http://dx.doi.org/10.1261/rna.030916.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3358649PMC
June 2012

B-cell ligand processing pathways detected by large-scale comparative analysis.

Genomics Proteomics Bioinformatics 2012 Jun 25;10(3):142-52. Epub 2012 Jun 25.

Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA 50010, USA.

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http://dx.doi.org/10.1016/j.gpb.2012.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054497PMC
June 2012

A global clustering algorithm to identify long intergenic non-coding RNA--with applications in mouse macrophages.

PLoS One 2011 30;6(9):e24051. Epub 2011 Sep 30.

Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184070PMC
April 2012

Gene-expression measurement: variance-modeling considerations for robust data analysis.

Nat Immunol 2012 Feb 16;13(3):199-203. Epub 2012 Feb 16.

Department of Bioengineering, University of California at San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1038/ni.2244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4358796PMC
February 2012

A complement-IL-4 regulatory circuit controls liver regeneration.

J Immunol 2012 Jan 19;188(2):641-8. Epub 2011 Dec 19.

Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.4049/jimmunol.1101925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3253144PMC
January 2012

LIPID MAPS-Nature Lipidomics Gateway: An Online Resource for Students and Educators Interested in Lipids.

J Chem Educ 2012 Jan;89(2):291-292

San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093 United States ; Departments of Bioengineering, Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 United States.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3995124PMC
January 2012

Modularity detection in protein-protein interaction networks.

BMC Res Notes 2011 Dec 29;4:569. Epub 2011 Dec 29.

Department of Bioengineering, University of California, San Diego, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3292542PMC
December 2011

Lipid classification, structures and tools.

Biochim Biophys Acta 2011 Nov 16;1811(11):637-47. Epub 2011 Jun 16.

University of California, San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1016/j.bbalip.2011.06.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3995129PMC
November 2011

Bioinformatics and systems biology of the lipidome.

Chem Rev 2011 Oct 23;111(10):6452-90. Epub 2011 Sep 23.

Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3383319PMC
October 2011

Pathways, networks, and systems medicine--the meeting place of the Aegean and the mind.

Wiley Interdiscip Rev Syst Biol Med 2011 May-Jun;3(3):253-4. Epub 2011 Apr 1.

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http://dx.doi.org/10.1002/wsbm.153DOI Listing
July 2011

Systems physiology--the heart of the matter or a bone of contention?

Wiley Interdiscip Rev Syst Biol Med 2011 Mar-Apr;3(2):127-8

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http://dx.doi.org/10.1002/wsbm.146DOI Listing
June 2011

Signaling gateway molecule pages--a data model perspective.

Bioinformatics 2011 Jun 19;27(12):1736-8. Epub 2011 Apr 19.

Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106186PMC
June 2011

MicroRNA-21 targets peroxisome proliferators-activated receptor-alpha in an autoregulatory loop to modulate flow-induced endothelial inflammation.

Proc Natl Acad Sci U S A 2011 Jun 2;108(25):10355-60. Epub 2011 Jun 2.

Department of Bioengineering and Institute of Engineering in Medicine, University of California at San Diego, La Jolla, CA 92032, USA.

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http://dx.doi.org/10.1073/pnas.1107052108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121870PMC
June 2011

Regulatory network of microRNAs in RAW 264.7 macrophage cells.

Conf Proc IEEE Eng Med Biol Soc 2010 ;2010:6198-201

Bioengineering Department of UC-San Diego, La Jolla, USA.

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March 2011

Systems biology and medicine--meta-issues and frameworks.

Wiley Interdiscip Rev Syst Biol Med 2010 Mar-Apr;2(2):i-ii

Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, OH.

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http://dx.doi.org/10.1002/wsbm.98DOI Listing
February 2011

Experimental selection of hypoxia-tolerant Drosophila melanogaster.

Proc Natl Acad Sci U S A 2011 Feb 24;108(6):2349-54. Epub 2011 Jan 24.

Department of Pediatrics, University of California at San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1073/pnas.1010643108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3038716PMC
February 2011

Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism.

BMC Syst Biol 2011 Feb 8;5:26. Epub 2011 Feb 8.

Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1186/1752-0509-5-26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047436PMC
February 2011

Systems biology--old wine in a new bottle or is the bottle changing the wine?

Wiley Interdiscip Rev Syst Biol Med 2010 Jan-Feb;2(1):1-2

Department of Bioengineering, University of California, San Diego, CA, USA.

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http://dx.doi.org/10.1002/wsbm.91DOI Listing
January 2011

Systems biology and medicine--metazoan life and processes.

Wiley Interdiscip Rev Syst Biol Med 2010 May-Jun;2(3):253-254

Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.

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http://dx.doi.org/10.1002/wsbm.99DOI Listing
January 2011

Multi-tissue, selective PPARγ modulation of insulin sensitivity and metabolic pathways in obese rats.

Am J Physiol Endocrinol Metab 2011 Jan 19;300(1):E164-74. Epub 2010 Oct 19.

Department of Bioengineering, University of California, San Diego, CA, USA.

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http://dx.doi.org/10.1152/ajpendo.00219.2010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023199PMC
January 2011

Systems medicine--viewed through the real and computing lenses.

Wiley Interdiscip Rev Syst Biol Med 2010 Jul-Aug;2(4):383-384

Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.

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http://dx.doi.org/10.1002/wsbm.103DOI Listing
December 2010

Stochastic hybrid modeling of intracellular calcium dynamics.

J Chem Phys 2010 Oct;133(16):165101

Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1063/1.3496996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998048PMC
October 2010