Shaojie Zhang

Shaojie Zhang

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Shaojie Zhang

Publications by authors named "Shaojie Zhang"

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An anti-windup INDI fault-tolerant control scheme for flying wing aircraft with actuator faults.

ISA Trans 2019 Oct 12;93:172-179. Epub 2019 Mar 12.

College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, Jiangsu, China.

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http://dx.doi.org/10.1016/j.isatra.2019.02.037DOI Listing
October 2019

Bis(propyl)-cognitin potentiates rehabilitation of treadmill exercise after a transient focal cerebral ischemia, possibly via inhibiting NMDA receptor and regulating VEGF expression.

Neurochem Int 2019 Sep 26;128:143-153. Epub 2019 Apr 26.

Interdisciplinary Division of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong; Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong. Electronic address:

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http://dx.doi.org/10.1016/j.neuint.2019.04.016DOI Listing
September 2019

Accurate and Efficient Mapping of the Cross-Linked microRNA-mRNA Duplex Reads.

iScience 2019 Aug 29;18:11-19. Epub 2019 May 29.

Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA.

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http://dx.doi.org/10.1016/j.isci.2019.05.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6609836PMC
August 2019

RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts.

Genome Biol 2019 07 25;20(1):143. Epub 2019 Jul 25.

School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s13059-019-1754-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6659282PMC
July 2019

Preparation of transparent anti-pollution cellulose carbamate regenerated cellulose membrane with high separation ability.

Int J Biol Macromol 2019 Jul 25;139:332-341. Epub 2019 Jul 25.

State Key Laboratory of Separation Membranes and Membrane Processes, School of Materials Science and Engineering, Tianjin Polytechnic University, Tianjin 300387, China. Electronic address:

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http://dx.doi.org/10.1016/j.ijbiomac.2019.07.146DOI Listing
July 2019

Efficient haplotype matching between a query and a panel for genealogical search.

Bioinformatics 2019 Jul;35(14):i233-i241

Department of Computer Science, University of Central Florida, Orlando, FL, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612857PMC
July 2019

SV40 seroprevalence in two Latin American countries involved in field trials of candidate oral poliovaccines.

J Infect 2019 Jun 6;78(6):476-483. Epub 2019 Apr 6.

Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, MS: BCM385, Houston, TX 77030, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01634453193011
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http://dx.doi.org/10.1016/j.jinf.2019.04.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544904PMC
June 2019

Multi-allelic positional Burrows-Wheeler transform.

BMC Bioinformatics 2019 Jun 6;20(Suppl 11):279. Epub 2019 Jun 6.

Department of Computer Science, University of Central Florida, Orlando, FL, 32816, USA.

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http://dx.doi.org/10.1186/s12859-019-2821-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6551244PMC
June 2019

Cell cycle- and genomic distance-dependent dynamics of a discrete chromosomal region.

J Cell Biol 2019 May 7;218(5):1467-1477. Epub 2019 Mar 7.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA

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http://dx.doi.org/10.1083/jcb.201807162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6504907PMC
May 2019

A fructooligosaccharide from Achyranthes bidentata inhibits osteoporosis by stimulating bone formation.

Carbohydr Polym 2019 Apr 9;210:110-118. Epub 2019 Jan 9.

School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China. Electronic address:

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http://dx.doi.org/10.1016/j.carbpol.2019.01.026DOI Listing
April 2019

Data on the convenient fabrication of carbon doped WO ultrathin nanosheets for photocatalytic aerobic oxidation of amines at room temperature.

Data Brief 2019 Apr 21;23:103624. Epub 2018 Dec 21.

Resource Environment & Clean Energy Laboratory, School of Chemical and Environmental Engineering, Jiangsu University of Technology, Changzhou 213001, China.

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http://dx.doi.org/10.1016/j.dib.2018.12.062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6370550PMC
April 2019

Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions.

Methods 2019 02 6;155:49-57. Epub 2018 Dec 6.

Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2018.12.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6387833PMC
February 2019

CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging.

Nat Methods 2018 11 30;15(11):928-931. Epub 2018 Oct 30.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.

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http://www.nature.com/articles/s41592-018-0174-0
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http://dx.doi.org/10.1038/s41592-018-0174-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6252086PMC
November 2018

The effects of resiquimod in an ovalbumin-induced allergic rhinitis model.

Int Immunopharmacol 2018 Jun 14;59:233-242. Epub 2018 Apr 14.

Department of Otorhinolaryngology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning 530021, China.

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http://dx.doi.org/10.1016/j.intimp.2018.04.015DOI Listing
June 2018

De novo discovery of structural motifs in RNA 3D structures through clustering.

Nucleic Acids Res 2018 05;46(9):4783-4793

Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA.

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http://dx.doi.org/10.1093/nar/gky139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5961109PMC
May 2018

Chemical modification of protein A chromatography ligands with polyethylene glycol. I: Effects on IgG adsorption equilibrium, kinetics, and transport.

J Chromatogr A 2018 Apr 9;1546:77-88. Epub 2018 Mar 9.

Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chroma.2018.03.011DOI Listing
April 2018

Chemical modification of protein a chromatography ligands with polyethylene glycol. II: Effects on resin robustness and process selectivity.

J Chromatogr A 2018 Apr 24;1546:89-96. Epub 2018 Feb 24.

Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00219673183018
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http://dx.doi.org/10.1016/j.chroma.2018.02.024DOI Listing
April 2018

Anti-osteoporosis activity of a novel Achyranthes bidentata polysaccharide via stimulating bone formation.

Carbohydr Polym 2018 Mar 30;184:288-298. Epub 2017 Dec 30.

School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China. Electronic address:

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http://dx.doi.org/10.1016/j.carbpol.2017.12.070DOI Listing
March 2018

DRREP: deep ridge regressed epitope predictor.

BMC Genomics 2017 Oct 3;18(Suppl 6):676. Epub 2017 Oct 3.

Department of Computer Science, University of Central Florida, Orlando, FL, USA.

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http://dx.doi.org/10.1186/s12864-017-4024-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629616PMC
October 2017

A Laboratory Experimental Study: An FBG-PVC Tube Integrated Device for Monitoring the Slip Surface of Landslides.

Sensors (Basel) 2017 Oct 30;17(11). Epub 2017 Oct 30.

Chongqing Institute of green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.

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http://dx.doi.org/10.3390/s17112486DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712886PMC
October 2017

Polyclonal and monoclonal IgG binding on protein A resins-Evidence of competitive binding effects.

Biotechnol Bioeng 2017 08 6;114(8):1803-1812. Epub 2017 Jun 6.

Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213.

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http://doi.wiley.com/10.1002/bit.26286
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http://dx.doi.org/10.1002/bit.26286DOI Listing
August 2017

CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures.

Nucleic Acids Res 2017 Aug;45(14):e136

Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA.

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http://dx.doi.org/10.1093/nar/gkx538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737500PMC
August 2017

Effects of 1,25-dihydroxyvitamin D3 in an ovalbumin-induced allergic rhinitis model.

Int Immunopharmacol 2017 Jun 13;47:182-189. Epub 2017 Apr 13.

Department of Otorhinolaryngology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning 530021, China.

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http://dx.doi.org/10.1016/j.intimp.2017.04.005DOI Listing
June 2017

Translation repression via modulation of the cytoplasmic poly(A)-binding protein in the inflammatory response.

Elife 2017 06 21;6. Epub 2017 Jun 21.

Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States.

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http://dx.doi.org/10.7554/eLife.27786DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5507668PMC
June 2017

Vehicle Counting and Moving Direction Identification Based on Small-Aperture Microphone Array.

Sensors (Basel) 2017 May 10;17(5). Epub 2017 May 10.

Science and Technology on Microsystem Laboratory, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 201800, China.

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http://dx.doi.org/10.3390/s17051089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5470479PMC
May 2017

Structural and performance characteristics of representative anion exchange resins used for weak partitioning chromatography.

Biotechnol Prog 2017 03 28;33(2):425-434. Epub 2017 Jan 28.

Dept. of Chemical Engineering, University of Virginia, Charlottesville, VA.

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http://doi.wiley.com/10.1002/btpr.2412
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http://dx.doi.org/10.1002/btpr.2412DOI Listing
March 2017

Advanced oxidation protein products induce endothelial-to-mesenchymal transition in human renal glomerular endothelial cells through induction of endoplasmic reticulum stress.

J Diabetes Complications 2016 May-Jun;30(4):573-9. Epub 2016 Jan 14.

Department of Nephrology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, Guangdong Province, China. Electronic address:

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http://dx.doi.org/10.1016/j.jdiacomp.2016.01.009DOI Listing
January 2017

Omeprazole induces heme oxygenase-1 in fetal human pulmonary microvascular endothelial cells via hydrogen peroxide-independent Nrf2 signaling pathway.

Toxicol Appl Pharmacol 2016 Nov 8;311:26-33. Epub 2016 Oct 8.

Division of Neonatal-Perinatal Medicine, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030, United States. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5089963PMC
http://dx.doi.org/10.1016/j.taap.2016.10.002DOI Listing
November 2016

Experimental Application of Bone Marrow Mesenchymal Stem Cells for the Repair of Intervertebral Disc Annulus Fibrosus.

Med Sci Monit 2016 Nov 18;22:4426-4430. Epub 2016 Nov 18.

Department of Anatomy, Basic Medical College, Inner Mongolia Medical University, Huhhot, Inner Mongolia, China (mainland).

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5124432PMC
http://dx.doi.org/10.12659/msm.898062DOI Listing
November 2016

CRISPR-Cas9 nuclear dynamics and target recognition in living cells.

J Cell Biol 2016 08 22;214(5):529-37. Epub 2016 Aug 22.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605

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http://www.jcb.org/lookup/doi/10.1083/jcb.201604115
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http://dx.doi.org/10.1083/jcb.201604115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5004447PMC
August 2016

Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow.

Nat Biotechnol 2016 05 18;34(5):528-30. Epub 2016 Apr 18.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.

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http://www.nature.com/articles/nbt.3526
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http://dx.doi.org/10.1038/nbt.3526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864854PMC
May 2016

Structural and functional characteristics of virgin and fouled Protein A MabSelect resin cycled in a monoclonal antibody purification process.

Biotechnol Bioeng 2016 Feb 3;113(2):367-75. Epub 2015 Sep 3.

Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, 22904.

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http://dx.doi.org/10.1002/bit.25708DOI Listing
February 2016

Nature of foulants and fouling mechanism in the Protein A MabSelect resin cycled in a monoclonal antibody purification process.

Biotechnol Bioeng 2016 Jan 18;113(1):141-9. Epub 2015 Oct 18.

Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia.

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http://dx.doi.org/10.1002/bit.25706DOI Listing
January 2016

Leflunomide Induces Pulmonary and Hepatic CYP1A Enzymes via Aryl Hydrocarbon Receptor.

Drug Metab Dispos 2015 Dec 28;43(12):1966-70. Epub 2015 Sep 28.

Section of Neonatology, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas

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http://dx.doi.org/10.1124/dmd.115.066084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658494PMC
December 2015

STAR3D: a stack-based RNA 3D structural alignment tool.

Nucleic Acids Res 2015 Nov 15;43(20):e137. Epub 2015 Jul 15.

Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816, USA

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http://dx.doi.org/10.1093/nar/gkv697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787758PMC
November 2015

Omeprazole Attenuates Pulmonary Aryl Hydrocarbon Receptor Activation and Potentiates Hyperoxia-Induced Developmental Lung Injury in Newborn Mice.

Toxicol Sci 2015 Nov 13;148(1):276-87. Epub 2015 Aug 13.

Section of Neonatal-Perinatal Medicine, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030.

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https://academic.oup.com/toxsci/article-lookup/doi/10.1093/t
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http://dx.doi.org/10.1093/toxsci/kfv183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4635634PMC
November 2015

Omeprazole induces NAD(P)H quinone oxidoreductase 1 via aryl hydrocarbon receptor-independent mechanisms: Role of the transcription factor nuclear factor erythroid 2-related factor 2.

Biochem Biophys Res Commun 2015 Nov 9;467(2):282-7. Epub 2015 Oct 9.

Section of Neonatology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2015.09.173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618076PMC
November 2015

Advanced oxidation protein products induce hypertrophy and epithelial-to-mesenchymal transition in human proximal tubular cells through induction of endoplasmic reticulum stress.

Cell Physiol Biochem 2015 30;35(2):816-28. Epub 2015 Jan 30.

Department of Nephrology, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China.

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http://dx.doi.org/10.1159/000369740DOI Listing
October 2015

Omeprazole does not Potentiate Acute Oxygen Toxicity in Fetal Human Pulmonary Microvascular Endothelial Cells Exposed to Hyperoxia.

Pharm Anal Acta 2015 Oct 9;6(10). Epub 2015 Oct 9.

Section of Neonatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.4172/2153-2435.1000424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4712726PMC
October 2015

ATF6 pathway of unfolded protein response mediates advanced oxidation protein product-induced hypertrophy and epithelial-to-mesenchymal transition in HK-2 cells.

Mol Cell Biochem 2015 Sep 5;407(1-2):197-207. Epub 2015 Jun 5.

Department of Nephrology, Zhujiang Hospital, Southern Medical University, No. 253, Gongye Road, Haizhu District, Guangzhou, 510280, Guangdong, China.

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http://dx.doi.org/10.1007/s11010-015-2469-0DOI Listing
September 2015

Adrenomedullin deficiency potentiates hyperoxic injury in fetal human pulmonary microvascular endothelial cells.

Biochem Biophys Res Commun 2015 Sep 18;464(4):1048-1053. Epub 2015 Jul 18.

Section of Neonatology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2015.07.067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4558361PMC
September 2015

Aryl hydrocarbon receptor is necessary to protect fetal human pulmonary microvascular endothelial cells against hyperoxic injury: Mechanistic roles of antioxidant enzymes and RelB.

Toxicol Appl Pharmacol 2015 Jul 29;286(2):92-101. Epub 2015 Mar 29.

Division of Neonatal-Perinatal Medicine, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.taap.2015.03.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458211PMC
July 2015

Computational analysis of RNA structures with chemical probing data.

Methods 2015 Jun 14;79-80:60-6. Epub 2015 Feb 14.

Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816-2362, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2015.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4437859PMC
June 2015

Discovering non-coding RNA elements in Drosophila 3' untranslated regions.

Int J Bioinform Res Appl 2014 ;10(4-5):479-97

Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816, USA.

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http://dx.doi.org/10.1504/IJBRA.2014.062996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121059PMC
March 2015

Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements.

Int J Bioinform Res Appl 2014 ;10(4-5):498-518

Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, Florida 32816, USA.

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http://dx.doi.org/10.1504/IJBRA.2014.062997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156590PMC
March 2015

RNAMotifScanX: a graph alignment approach for RNA structural motif identification.

RNA 2015 Mar 16;21(3):333-46. Epub 2015 Jan 16.

Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, Florida 32816, USA

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http://dx.doi.org/10.1261/rna.044891.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338331PMC
March 2015

Multicolor CRISPR labeling of chromosomal loci in human cells.

Proc Natl Acad Sci U S A 2015 Mar 23;112(10):3002-7. Epub 2015 Feb 23.

Program in Cell and Developmental Dynamics and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605;

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http://dx.doi.org/10.1073/pnas.1420024112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364232PMC
March 2015

Simultaneous folding of alternative RNA structures with mutual constraints: an application to next-generation sequencing-based RNA structure probing.

J Comput Biol 2014 Aug 1;21(8):609-21. Epub 2014 Apr 1.

Department of Electrical Engineering and Computer Science, University of Central Florida , Orlando, Florida.

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http://dx.doi.org/10.1089/cmb.2013.0044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116156PMC
August 2014

Unfolding and aggregation of a glycosylated monoclonal antibody on a cation exchange column. Part I. Chromatographic elution and batch adsorption behavior.

J Chromatogr A 2014 Aug 19;1356:117-28. Epub 2014 Jun 19.

Department of Chemical Engineering, University of Virginia, Charlottesville, VA 22904, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00219673140096
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http://dx.doi.org/10.1016/j.chroma.2014.06.037DOI Listing
August 2014

A memory efficient method for structure-based RNA multiple alignment.

IEEE/ACM Trans Comput Biol Bioinform 2012 Jan-Feb;9(1):1-11. Epub 2011 Apr 29.

University of Central Florida, Orlando.

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http://dx.doi.org/10.1109/TCBB.2011.86DOI Listing
April 2014

Cis-suppression to arrest protein aggregation in mammalian cells.

Biotechnol Bioeng 2014 Mar 18;111(3):462-74. Epub 2013 Oct 18.

Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, 22904-4741.

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http://dx.doi.org/10.1002/bit.25119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4492694PMC
March 2014

Viral microRNA effects on pathogenesis of polyomavirus SV40 infections in syrian golden hamsters.

PLoS Pathog 2014 Feb 6;10(2):e1003912. Epub 2014 Feb 6.

Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1003912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3916418PMC
February 2014

Overexpression of mitochondrial uncoupling protein conferred resistance to heat stress and Botrytis cinerea infection in tomato.

Plant Physiol Biochem 2013 Dec 17;73:245-53. Epub 2013 Oct 17.

College of Forestry, Henan University of Science and Technology, Luoyang 471003, PR China. Electronic address:

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http://dx.doi.org/10.1016/j.plaphy.2013.10.002DOI Listing
December 2013

Efficient alignment of RNA secondary structures using sparse dynamic programming.

BMC Bioinformatics 2013 Sep 8;14:269. Epub 2013 Sep 8.

Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816-2362, USA.

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http://dx.doi.org/10.1186/1471-2105-14-269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3871798PMC
September 2013

Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction.

BMC Bioinformatics 2013 Apr 27;14:142. Epub 2013 Apr 27.

Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816-2362, USA.

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http://dx.doi.org/10.1186/1471-2105-14-142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691524PMC
April 2013

Evaluation of transcranial Doppler flow velocity changes in intracerebral hemorrhage rats using ultrasonography.

J Neurosci Methods 2012 Sep 9;210(2):272-80. Epub 2012 Aug 9.

Interdisciplinary Division of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region.

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http://dx.doi.org/10.1016/j.jneumeth.2012.07.024DOI Listing
September 2012

Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data.

BMC Genomics 2012 Aug 21;13:412. Epub 2012 Aug 21.

Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816, USA.

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http://dx.doi.org/10.1186/1471-2164-13-412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3478165PMC
August 2012

Predicting folding pathways between RNA conformational structures guided by RNA stacks.

BMC Bioinformatics 2012 Mar 21;13 Suppl 3:S5. Epub 2012 Mar 21.

Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816-2362, USA.

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http://dx.doi.org/10.1186/1471-2105-13-S3-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402921PMC
March 2012

Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment.

Nucleic Acids Res 2012 Feb 5;40(3):1307-17. Epub 2011 Oct 5.

Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816, USA.

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http://dx.doi.org/10.1093/nar/gkr804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273805PMC
February 2012

Finding stable local optimal RNA secondary structures.

Bioinformatics 2011 Nov 8;27(21):2994-3001. Epub 2011 Sep 8.

Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr510DOI Listing
November 2011

Epigenetic regulation of microRNA-375 and its role in melanoma development in humans.

FEBS Lett 2011 Aug 26;585(15):2467-76. Epub 2011 Jun 26.

Sanford Burnham Medical Research Institute, Orlando, FL 32827, United States.

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http://dx.doi.org/10.1016/j.febslet.2011.06.025DOI Listing
August 2011

[Analysis with the logistic regression mode to the audiologic and vestibular functions in Meniere's disease].

Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2011 May;25(10):452-6

Department of Otorhinolaryngology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.

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May 2011

RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment.

Nucleic Acids Res 2010 Oct 8;38(18):e176. Epub 2010 Aug 8.

School of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816, USA.

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http://dx.doi.org/10.1093/nar/gkq672DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952876PMC
October 2010

A large intrinsically disordered region in SKIP and its disorder-order transition induced by PPIL1 binding revealed by NMR.

J Biol Chem 2010 Feb 9;285(7):4951-63. Epub 2009 Dec 9.

Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.

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http://dx.doi.org/10.1074/jbc.M109.087528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836099PMC
February 2010

Structural alignment of pseudoknotted RNA.

J Comput Biol 2008 Jun;15(5):489-504

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1089/cmb.2007.0214DOI Listing
June 2008

Searching genomes for noncoding RNA using FastR.

IEEE/ACM Trans Comput Biol Bioinform 2005 Oct-Dec;2(4):366-79

Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0114, USA.

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http://dx.doi.org/10.1109/TCBB.2005.57DOI Listing
October 2006

FastR: fast database search tool for non-coding RNA.

Proc IEEE Comput Syst Bioinform Conf 2004 :52-61

Department of Computer Science and Engineering, University of California at San Diego, La Jolla, 92093-0114, USA.

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July 2006

A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements.

Bioinformatics 2006 Jul;22(14):e557-65

Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btl232DOI Listing
July 2006

Consensus folding of unaligned RNA sequences revisited.

J Comput Biol 2006 Mar;13(2):283-95

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, 92093, USA.

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http://dx.doi.org/10.1089/cmb.2006.13.283DOI Listing
March 2006

Quantification of vertical transmission of Murine polyoma virus by real-time quantitative PCR.

J Gen Virol 2005 Oct;86(Pt 10):2721-9

Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, MS BCM385, Houston, TX 77030, USA.

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http://dx.doi.org/10.1099/vir.0.81168-0DOI Listing
October 2005

Effects of radiation and latent virus on immune responses in a space flight model.

J Allergy Clin Immunol 2005 Jun;115(6):1297-303

Department of Pediatrics, Section of Allergy and Immunology, Baylor College of Medicine, Houston, TX, USA.

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http://dx.doi.org/10.1016/j.jaci.2005.03.003DOI Listing
June 2005

[Analysis of urban forest landscape pattern in Hefei].

Ying Yong Sheng Tai Xue Bao 2003 Dec;14(12):2117-22

Forestry Faculty of Anhui Agricultural University, Hefei 230036, China.

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December 2003