Tariq M Rana

Tariq M Rana

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Tariq M Rana

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Integrin αvβ5 Internalizes Zika Virus during Neural Stem Cells Infection and Provides a Promising Target for Antiviral Therapy.

Cell Rep 2020 Jan 13. Epub 2020 Jan 13.

Division of Genetics, Department of Pediatrics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego School of Medicine, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Biology, Bioinformatics Program, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.11.020DOI Listing
January 2020

The Long Noncoding RNA Regulates HIV-1 Replication through Epigenetic Regulation of the HIV-1 Promoter.

mBio 2019 09 24;10(5). Epub 2019 Sep 24.

Division of Genetics, Department of Pediatrics, UCSD Center for AIDS Research, and Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA

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http://dx.doi.org/10.1128/mBio.02016-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6759764PMC
September 2019

Genome-wide Integrative Analysis of Zika-Virus-Infected Neuronal Stem Cells Reveals Roles for MicroRNAs in Cell Cycle and Stemness.

Cell Rep 2019 Jun;27(12):3618-3628.e5

Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA; Division of Genetics, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA; Program in Immunology, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, 9500 Gilman Drive, MC 0762, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.05.059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6687627PMC
June 2019

Profiling of N-Methyladenosine in Zika Virus RNA and Host Cellular mRNA.

Methods Mol Biol 2019 ;1870:209-218

Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.

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http://link.springer.com/10.1007/978-1-4939-8808-2_16
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http://dx.doi.org/10.1007/978-1-4939-8808-2_16DOI Listing
May 2019

HIV-1 Escape from Small-Molecule Antagonism of Vif.

mBio 2019 02 26;10(1). Epub 2019 Feb 26.

Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA

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http://dx.doi.org/10.1128/mBio.00144-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391917PMC
February 2019

Next-Generation Sequencing of Genome-Wide CRISPR Screens.

Methods Mol Biol 2018 ;1712:203-216

Solid Tumor Therapeutics Program, Moores Cancer Center, University of California, San Diego, 3855 Health Sciences Drive, La Jolla, CA, 92093, USA.

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http://dx.doi.org/10.1007/978-1-4939-7514-3_13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6089254PMC
July 2018

Lipoprotein lipase regulates hematopoietic stem progenitor cell maintenance through DHA supply.

Nat Commun 2018 04 3;9(1):1310. Epub 2018 Apr 3.

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

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http://dx.doi.org/10.1038/s41467-018-03775-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5882990PMC
April 2018

Genome-Wide CRISPR Screen for Essential Cell Growth Mediators in Mutant KRAS Colorectal Cancers.

Cancer Res 2017 11 27;77(22):6330-6339. Epub 2017 Sep 27.

Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-2043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5690866PMC
November 2017

Zika virus infection reprograms global transcription of host cells to allow sustained infection.

Emerg Microbes Infect 2017 Apr 26;6(4):e24. Epub 2017 Apr 26.

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

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http://dx.doi.org/10.1038/emi.2017.9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5457678PMC
April 2017

Identification of novel genes and networks governing hematopoietic stem cell development.

EMBO Rep 2016 12 26;17(12):1814-1828. Epub 2016 Oct 26.

Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA

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http://dx.doi.org/10.15252/embr.201642395DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167341PMC
December 2016

Dynamics of Human and Viral RNA Methylation during Zika Virus Infection.

Cell Host Microbe 2016 Nov 20;20(5):666-673. Epub 2016 Oct 20.

Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Program for RNA Biology and Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2016.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5155635PMC
November 2016

A Herpesvirus Protein Selectively Inhibits Cellular mRNA Nuclear Export.

Cell Host Microbe 2016 Nov;20(5):642-653

Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2016.10.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5130111PMC
November 2016

miR-34 Modulates Innate Immunity and Ecdysone Signaling in Drosophila.

PLoS Pathog 2016 Nov 28;12(11):e1006034. Epub 2016 Nov 28.

Tumor Initiation and Maintenance Program; Sanford Burnham Prebys Medical Discovery Institute, California, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1006034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5125713PMC
November 2016

Enhancing Induced Pluripotent Stem Cell Generation by MicroRNA.

Methods Mol Biol 2016 ;1357:71-84

Department of Pediatrics, University of California San Diego School of Medicine, 9500 Gilman Drive MC 0762, La Jolla, CA, 92093, USA.

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http://link.springer.com/10.1007/7651_2015_201
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http://dx.doi.org/10.1007/7651_2015_201DOI Listing
October 2016

miR-1298 Inhibits Mutant KRAS-Driven Tumor Growth by Repressing FAK and LAMB3.

Cancer Res 2016 10;76(19):5777-5787

Program for RNA Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California. Department of Pediatrics, University of California San Diego, La Jolla, California. Solid Tumor Therapeutics Program, Moores Cancer Center, University of California, San Diego, La Jolla, California. Institute for Genomic Medicine, University of California San Diego, La Jolla, California.

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http://dx.doi.org/10.1158/0008-5472.CAN-15-2936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5155639PMC
October 2016

Zika Virus Depletes Neural Progenitors in Human Cerebral Organoids through Activation of the Innate Immune Receptor TLR3.

Cell Stem Cell 2016 08 6;19(2):258-265. Epub 2016 May 6.

Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2016.04.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5116380PMC
August 2016

1,2,3-Triazoles as Amide Bioisosteres: Discovery of a New Class of Potent HIV-1 Vif Antagonists.

J Med Chem 2016 08 10;59(16):7677-82. Epub 2016 Aug 10.

Program for RNA Biology, Sanford Burnham Prebys Medical Discovery Institute , La Jolla, California 92037, United States.

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http://dx.doi.org/10.1021/acs.jmedchem.6b00247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534211PMC
August 2016

Polycomb Group Protein Pcgf6 Acts as a Master Regulator to Maintain Embryonic Stem Cell Identity.

Sci Rep 2016 06 1;6:26899. Epub 2016 Jun 1.

Department of Pediatrics, University of California San Diego School of Medicine, 9500 Gilman Drive MC 0762, La Jolla, California, 92093, USA.

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http://dx.doi.org/10.1038/srep26899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4888081PMC
June 2016

Dynamics of the human and viral m(6)A RNA methylomes during HIV-1 infection of T cells.

Nat Microbiol 2016 Feb 22;1:16011. Epub 2016 Feb 22.

Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nmicrobiol.2016.11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6053355PMC
February 2016

Decoding the noncoding: prospective of lncRNA-mediated innate immune regulation.

RNA Biol 2014 31;11(8):979-85. Epub 2014 Oct 31.

a Program for RNA Biology; Sanford-Burnham Medical Research Institute ; La Jolla , CA USA.

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http://dx.doi.org/10.4161/rna.29937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615744PMC
August 2015

Haunting the HOXA Locus: Two Faces of lncRNA Regulation.

Cell Stem Cell 2015 May;16(5):449-50

Department of Pediatrics, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA. Electronic address:

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http://www.cell.com/cell-stem-cell/pdf/S1934-5909(15)00168-X
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http://linkinghub.elsevier.com/retrieve/pii/S193459091500168
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http://dx.doi.org/10.1016/j.stem.2015.04.010DOI Listing
May 2015

Preparation of novel curdlan nanoparticles for intracellular siRNA delivery.

Carbohydr Polym 2015 Mar 5;117:324-30. Epub 2014 Oct 5.

School of Chemistry & Chemical Engineering, Inner Mongolia University, 235 West College Road, Hohhot, Inner Mongolia, 010020, PR China; Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.carbpol.2014.09.069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4268549PMC
March 2015

MicroRNA-mediated regulation of extracellular matrix formation modulates somatic cell reprogramming.

RNA 2014 Dec 21;20(12):1900-15. Epub 2014 Oct 21.

Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California 92093, USA

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http://dx.doi.org/10.1261/rna.043745.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4238355PMC
December 2014

Strategies to antagonize miRNA functions in vitro and in vivo.

Nanomedicine (Lond) 2014 Nov;9(16):2545-55

Department of Applied Chemistry, School of Chemistry & Chemical Engineering, Inner Mongolia University, 235 West College Road, Hohhot 010021, China.

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http://dx.doi.org/10.2217/nnm.14.162DOI Listing
November 2014

Gene regulation by non-coding RNAs.

Crit Rev Biochem Mol Biol 2014 Jan-Feb;49(1):16-32. Epub 2013 Oct 28.

Program for RNA Biology, Sanford-Burnham Medical Research Institute , La Jolla, CA , USA .

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http://dx.doi.org/10.3109/10409238.2013.844092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4721600PMC
September 2014

Therapeutic targeting of microRNAs: current status and future challenges.

Nat Rev Drug Discov 2014 Aug 11;13(8):622-38. Epub 2014 Jul 11.

1] Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA. [2] Department of Pediatrics, University of California San Diego School of Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, USA.

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http://www.nature.com/articles/nrd4359
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http://dx.doi.org/10.1038/nrd4359DOI Listing
August 2014

Genome-wide functional analysis reveals factors needed at the transition steps of induced reprogramming.

Cell Rep 2014 Jul 17;8(2):327-37. Epub 2014 Jul 17.

Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Pediatrics, University of California San Diego School of Medicine, 9500 Gilman Drive, Mail Code 0762, La Jolla, CA 92093, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247140056
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http://dx.doi.org/10.1016/j.celrep.2014.07.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4152236PMC
July 2014

Kinome-wide functional analysis highlights the role of cytoskeletal remodeling in somatic cell reprogramming.

Cell Stem Cell 2014 Apr;14(4):523-34

Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Pediatrics, Rady Children's Hospital San Diego and University of California San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2014.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071169PMC
April 2014

An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment.

Mol Cell 2014 Mar 13;53(6):1005-19. Epub 2014 Feb 13.

Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Pediatrics, Rady Children's Hospital San Diego and University of California San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.01.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010157PMC
March 2014

The long noncoding RNA THRIL regulates TNFα expression through its interaction with hnRNPL.

Proc Natl Acad Sci U S A 2014 Jan 26;111(3):1002-7. Epub 2013 Dec 26.

Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037.

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http://dx.doi.org/10.1073/pnas.1313768111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3903238PMC
January 2014

Testing the substrate-envelope hypothesis with designed pairs of compounds.

ACS Chem Biol 2013 Nov 26;8(11):2433-41. Epub 2013 Sep 26.

Department of Biological Engineering, ‡Department of Chemistry, and ○Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.

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http://dx.doi.org/10.1021/cb400468cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833293PMC
November 2013

Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration.

J Chem Theory Comput 2013 Nov 7;9(11):5098-5115. Epub 2013 Aug 7.

Department of Chemistry and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.

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http://dx.doi.org/10.1021/ct400383vDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827837PMC
November 2013

Core small nuclear ribonucleoprotein particle splicing factor SmD1 modulates RNA interference in Drosophila.

Proc Natl Acad Sci U S A 2013 Oct 25;110(41):16520-5. Epub 2013 Sep 25.

Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037.

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http://dx.doi.org/10.1073/pnas.1315803110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799365PMC
October 2013

Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance.

Chem Biol 2013 Sep 5;20(9):1116-24. Epub 2013 Sep 5.

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

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http://dx.doi.org/10.1016/j.chembiol.2013.07.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3934494PMC
September 2013

In Vivo Delivery of RNAi by Reducible Interfering Nanoparticles (iNOPs).

ACS Med Chem Lett 2013 Aug 18;4(8):720-723. Epub 2013 Jun 18.

Program for RNA Biology, Sanford-Burnham Medical Research Institute , 10901 North Torrey Pines Road, La Jolla, California 92037, United States ; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States.

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http://dx.doi.org/10.1021/ml4001003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3850243PMC
August 2013

RNA-based mechanisms regulating host-virus interactions.

Immunol Rev 2013 May;253(1):97-111

Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1111/imr.12053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695692PMC
May 2013

A kinase inhibitor screen identifies small-molecule enhancers of reprogramming and iPS cell generation.

Nat Commun 2012 ;3:1085

Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA.

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http://www.nature.com/articles/ncomms2059
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http://dx.doi.org/10.1038/ncomms2059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658009PMC
February 2013

Learning the molecular mechanisms of the reprogramming factors: let's start from microRNAs.

Mol Biosyst 2013 Jan 5;9(1):10-7. Epub 2012 Oct 5.

Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1039/c2mb25088hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3933261PMC
January 2013

Using microRNAs to enhance the generation of induced pluripotent stem cells.

Curr Protoc Stem Cell Biol 2012 ;Chapter 4:Unit 4A.4

Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, California, USA.

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http://dx.doi.org/10.1002/9780470151808.sc04a04s20DOI Listing
September 2012

Interfering nanoparticles for silencing microRNAs.

Methods Enzymol 2012 ;509:339-53

Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, California, USA.

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http://dx.doi.org/10.1016/B978-0-12-391858-1.00017-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3933207PMC
August 2012

Molecular mechanisms of RNA-triggered gene silencing machineries.

Acc Chem Res 2012 Jul 3;45(7):1122-31. Epub 2012 Feb 3.

Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States.

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http://dx.doi.org/10.1021/ar200253uDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398549PMC
July 2012

Deep annotation of mouse iso-miR and iso-moR variation.

Nucleic Acids Res 2012 Jul 19;40(13):5864-75. Epub 2012 Mar 19.

Neuroscience Research Institute and Department of Cellular Molecular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.

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http://dx.doi.org/10.1093/nar/gks247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3401436PMC
July 2012

Synthesis and structure-activity relationship studies of HIV-1 virion infectivity factor (Vif) inhibitors that block viral replication.

ChemMedChem 2012 Jul 3;7(7):1217-29. Epub 2012 May 3.

Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1002/cmdc.201200079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517065PMC
July 2012

miR-TRAP: a benchtop chemical biology strategy to identify microRNA targets.

Angew Chem Int Ed Engl 2012 Jun 8;51(24):5880-3. Epub 2012 May 8.

Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1002/anie.201201512DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3501383PMC
June 2012

SAR and Lead Optimization of an HIV-1 Vif-APOBEC3G Axis Inhibitor.

ACS Med Chem Lett 2012 Jun;3(6):465-469

Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, California 92037 (USA).

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http://dx.doi.org/10.1021/ml300037kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3922209PMC
June 2012

Phosphorylation of histone H1 by P-TEFb is a necessary step in skeletal muscle differentiation.

J Cell Physiol 2012 Jan;227(1):383-9

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

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http://doi.wiley.com/10.1002/jcp.22797
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http://dx.doi.org/10.1002/jcp.22797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562545PMC
January 2012

Discovery of nonsteroidal anti-inflammatory drug and anticancer drug enhancing reprogramming and induced pluripotent stem cell generation.

Stem Cells 2011 Oct;29(10):1528-36

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

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http://doi.wiley.com/10.1002/stem.717
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http://dx.doi.org/10.1002/stem.717DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419601PMC
October 2011

microRNAs modulate iPS cell generation.

RNA 2011 Aug 21;17(8):1451-60. Epub 2011 Jun 21.

Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1261/rna.2664111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3153970PMC
August 2011

Silencing microRNA by interfering nanoparticles in mice.

Nucleic Acids Res 2011 Mar 6;39(6):e38. Epub 2011 Jan 6.

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

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http://dx.doi.org/10.1093/nar/gkq1307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064800PMC
March 2011

Small RNA-mediated regulation of iPS cell generation.

EMBO J 2011 Mar 1;30(5):823-34. Epub 2011 Feb 1.

Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/emboj.2011.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3049216PMC
March 2011

MicroRNAs encoded by Kaposi's sarcoma-associated herpesvirus regulate viral life cycle.

EMBO Rep 2010 Oct 17;11(10):784-90. Epub 2010 Sep 17.

Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/embor.2010.132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2948186PMC
October 2010

P-TEFb kinase complex phosphorylates histone H1 to regulate expression of cellular and HIV-1 genes.

J Biol Chem 2010 Sep 15;285(39):29713-20. Epub 2010 Jun 15.

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

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http://dx.doi.org/10.1074/jbc.M110.125997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943301PMC
September 2010

Design and assembly of new nonviral RNAi delivery agents by microwave-assisted quaternization (MAQ) of tertiary amines.

Bioconjug Chem 2010 Sep;21(9):1581-7

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012264PMC
September 2010

LIM-domain proteins, LIMD1, Ajuba, and WTIP are required for microRNA-mediated gene silencing.

Proc Natl Acad Sci U S A 2010 Jul 28;107(28):12499-504. Epub 2010 Jun 28.

School of Biomedical Sciences, University of Nottingham Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom.

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http://dx.doi.org/10.1073/pnas.0914987107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906597PMC
July 2010

Nanotubes functionalized with lipids and natural amino acid dendrimers: a new strategy to create nanomaterials for delivering systemic RNAi.

Bioconjug Chem 2010 Jan;21(1):56-63

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

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http://dx.doi.org/10.1021/bc900296zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2814541PMC
January 2010

Delivery of therapeutic RNAi by nanovehicles.

Chembiochem 2009 Oct;10(15):2449-54

Program for RNA Biology, Sanford Children's Health Research Center, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1002/cbic.200900252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517099PMC
October 2009

Identification of flavopiridol analogues that selectively inhibit positive transcription elongation factor (P-TEFb) and block HIV-1 replication.

Chembiochem 2009 Aug;10(12):2072-80

Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 (USA).

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http://dx.doi.org/10.1002/cbic.200900303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754223PMC
August 2009

Cellular microRNA and P bodies modulate host-HIV-1 interactions.

Mol Cell 2009 Jun;34(6):696-709

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1016/j.molcel.2009.06.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763548PMC
June 2009

U30 of 7SK RNA forms a specific photo-cross-link with Hexim1 in the context of both a minimal RNA-binding site and a fully reconstituted 7SK/Hexim1/P-TEFb ribonucleoprotein complex.

J Mol Biol 2009 Mar;386(4):1094-107

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-2324, USA.

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http://dx.doi.org/10.1016/j.jmb.2009.01.015DOI Listing
March 2009

Additivity in the analysis and design of HIV protease inhibitors.

J Med Chem 2009 Feb;52(3):737-54

Center for Advanced Research in Biotechnology, UMBI, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA.

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http://dx.doi.org/10.1021/jm8009525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715819PMC
February 2009

Small-molecule inhibition of HIV-1 Vif.

Nat Biotechnol 2008 Oct 21;26(10):1187-92. Epub 2008 Sep 21.

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

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http://dx.doi.org/10.1038/nbt.1496DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2693000PMC
October 2008

Potent RNAi by short RNA triggers.

RNA 2008 Sep 24;14(9):1714-9. Epub 2008 Jul 24.

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

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http://dx.doi.org/10.1261/rna.1161908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2525957PMC
September 2008

Evolutionary emergence of microRNAs in human embryonic stem cells.

PLoS One 2008 Jul 30;3(7):e2820. Epub 2008 Jul 30.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002820PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2474702PMC
July 2008

Therapeutic gene silencing delivered by a chemically modified small interfering RNA against mutant SOD1 slows amyotrophic lateral sclerosis progression.

J Biol Chem 2008 Jun 26;283(23):15845-52. Epub 2008 Mar 26.

Department of Biochemistry and Molecular Pharmacology, Chemical Biology Program, Cell Biology, and Neuroscience Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

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http://dx.doi.org/10.1074/jbc.M800834200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2414310PMC
June 2008

Small RNAs: regulators and guardians of the genome.

J Cell Physiol 2007 Nov;213(2):412-9

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

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http://dx.doi.org/10.1002/jcp.21230DOI Listing
November 2007

Design and synthesis of HIV-1 protease inhibitors incorporating oxazolidinones as P2/P2' ligands in pseudosymmetric dipeptide isosteres.

J Med Chem 2007 Sep 16;50(18):4316-28. Epub 2007 Aug 16.

Chemical Biology Program and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

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http://dx.doi.org/10.1021/jm070284zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3862176PMC
September 2007

RNA helicase A interacts with RISC in human cells and functions in RISC loading.

Mol Cell 2007 May;26(4):523-37

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

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May 2007

Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis.

Chem Biol Drug Des 2007 May;69(5):298-313

Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1111/j.1747-0285.2007.00514.xDOI Listing
May 2007

Quantitative analysis of RNA-mediated protein-protein interactions in living cells by FRET.

Chem Biol Drug Des 2007 Apr;69(4):233-9

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

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April 2007

Illuminating the silence: understanding the structure and function of small RNAs.

Authors:
Tariq M Rana

Nat Rev Mol Cell Biol 2007 Jan;8(1):23-36

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

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http://www.nature.com/articles/nrm2085
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January 2007

Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands.

J Med Chem 2006 Dec;49(25):7342-56

Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

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http://pubs.acs.org/doi/abs/10.1021/jm060666p
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December 2006

Dynamics of nascent mRNA folding and RNA-protein interactions: an alternative TAR RNA structure is involved in the control of HIV-1 mRNA transcription.

Nucleic Acids Res 2006 18;34(15):4278-92. Epub 2006 Aug 18.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-2324, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkl499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1616951PMC
October 2006

Orientation and affinity of HIV-1 Tat fragments in Tat-TAR complex determined by fluorescence resonance energy transfer.

Bioconjug Chem 2006 Mar-Apr;17(2):352-8

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

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July 2006

Translation repression in human cells by microRNA-induced gene silencing requires RCK/p54.

PLoS Biol 2006 Jul;4(7):e210

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

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http://dx.doi.org/10.1371/journal.pbio.0040210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1475773PMC
July 2006

Human retroviral host restriction factors APOBEC3G and APOBEC3F localize to mRNA processing bodies.

PLoS Pathog 2006 May 12;2(5):e41. Epub 2006 May 12.

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

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http://dx.doi.org/10.1371/journal.ppat.0020041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1458959PMC
May 2006

Design, microwave-assisted synthesis, and photophysical properties of small molecule organic antennas for luminescence resonance energy transfer.

J Comb Chem 2005 Mar-Apr;7(2):279-84

Program in Chemical Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA.

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http://pubs.acs.org/doi/abs/10.1021/cc0498480
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February 2006

Design and synthesis of a novel peptidomimetic inhibitor of HIV-1 Tat-TAR interactions: squaryldiamide as a new potential bioisostere of unsubstituted guanidine.

Bioorg Med Chem Lett 2005 Oct;15(19):4243-6

Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-2324, USA.

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http://dx.doi.org/10.1016/j.bmcl.2005.06.077DOI Listing
October 2005

Dissecting RNA-interference pathway with small molecules.

Chem Biol 2005 Jun;12(6):643-8

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

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http://dx.doi.org/10.1016/j.chembiol.2005.04.016DOI Listing
June 2005

Solid-phase synthesis of alpha-(2-(benzylthio)-1,4-dihydro-6-methyl-4-p-tolylpyrimidine-5-carboxamido) acids: a new strategy to create diversity in heterocyclic scaffolds.

J Comb Chem 2004 Jul-Aug;6(4):457-9

Program in Chemical Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA.

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http://pubs.acs.org/doi/abs/10.1021/cc034064s
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May 2005

Microwave-assisted parallel synthesis of a 4,6-diamino-2,2-dimethyl-1,2-dihydro-1-phenyl-s-triazine library.

J Comb Chem 2004 Jul-Aug;6(4):504-8

Program in Chemical Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA.

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http://pubs.acs.org/doi/abs/10.1021/cc049950x
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May 2005

Target accessibility dictates the potency of human RISC.

Nat Struct Mol Biol 2005 May 24;12(5):469-70. Epub 2005 Apr 24.

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

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http://dx.doi.org/10.1038/nsmb931DOI Listing
May 2005

Analysis of HIV-1 viral infectivity factor-mediated proteasome-dependent depletion of APOBEC3G: correlating function and subcellular localization.

J Biol Chem 2005 Mar 10;280(9):8387-96. Epub 2004 Nov 10.

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

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http://www.jbc.org/lookup/doi/10.1074/jbc.M408048200
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March 2005

Specific and potent RNAi in the nucleus of human cells.

Nat Struct Mol Biol 2005 Feb 9;12(2):133-7. Epub 2005 Jan 9.

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

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http://www.nature.com/articles/nsmb886
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February 2005

Mechanism of site-specific psoralen photoadducts formation in triplex DNA directed by psoralen-conjugated oligonucleotides.

Biochemistry 2005 Feb;44(7):2501-9

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

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https://pubs.acs.org/doi/10.1021/bi0488707
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February 2005

Modulating HIV-1 replication by RNA interference directed against human transcription elongation factor SPT5.

Retrovirology 2004 Dec 27;1:46. Epub 2004 Dec 27.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1186/1742-4690-1-46DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC545048PMC
December 2004

Visualizing a correlation between siRNA localization, cellular uptake, and RNAi in living cells.

Chem Biol 2004 Aug;11(8):1165-75

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

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http://dx.doi.org/10.1016/j.chembiol.2004.06.006DOI Listing
August 2004

Inhibition of human immunodeficiency virus type 1 replication by RNA interference directed against human transcription elongation factor P-TEFb (CDK9/CyclinT1).

J Virol 2004 Mar;78(5):2517-29

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC369228PMC
http://dx.doi.org/10.1128/jvi.78.5.2517-2529.2004DOI Listing
March 2004

Discovery of a small molecule Tat-trans-activation-responsive RNA antagonist that potently inhibits human immunodeficiency virus-1 replication.

J Biol Chem 2003 Oct 11;278(40):39092-103. Epub 2003 Jul 11.

Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605-2324, USA.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M301749200
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October 2003

Selective binding of TAR RNA by a Tat-derived beta-peptide.

Org Lett 2003 Oct;5(20):3563-5

Department of Chemistry and Medical Scientist Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1021/ol034977vDOI Listing
October 2003

siRNA function in RNAi: a chemical modification analysis.

RNA 2003 Sep;9(9):1034-48

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370469PMC
http://dx.doi.org/10.1261/rna.5103703DOI Listing
September 2003