Publications by authors named "Ravi Sachidanandam"

100Publications

PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription.

Nucleic Acids Res 2019 06;47(11):5573-5586

Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1470 Author afMadison Avenue, New York, NY 10029, USA.

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https://academic.oup.com/nar/article/47/11/5573/5477455
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http://dx.doi.org/10.1093/nar/gkz272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582409PMC
June 2019

Clonal Deletion of Tumor-Specific T Cells by Interferon-γ Confers Therapeutic Resistance to Combination Immune Checkpoint Blockade.

Immunity 2019 02 5;50(2):477-492.e8. Epub 2019 Feb 5.

Department of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2019.01.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6886475PMC
February 2019

SHP2 Drives Adaptive Resistance to ERK Signaling Inhibition in Molecularly Defined Subsets of ERK-Dependent Tumors.

Cell Rep 2019 01;26(1):65-78.e5

Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.12.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396678PMC
January 2019

Exonuclease Domain-Containing 1 Enhances MIWI2 piRNA Biogenesis via Its Interaction with TDRD12.

Cell Rep 2018 09;24(13):3423-3432.e4

Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.08.087DOI Listing
September 2018

Unperturbed expression bias of imprinted genes in schizophrenia.

Nat Commun 2018 07 25;9(1):2914. Epub 2018 Jul 25.

Department of Cell, Developmental and Regenerative Biology, ISMMS, New York, NY, 10029, USA.

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http://dx.doi.org/10.1038/s41467-018-04960-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6060121PMC
July 2018

Quiescent Tissue Stem Cells Evade Immune Surveillance.

Immunity 2018 02;48(2):271-285.e5

Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10747613183003
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http://dx.doi.org/10.1016/j.immuni.2018.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5824652PMC
February 2018

Regulation of mA Transcripts by the 3'→5' RNA Helicase YTHDC2 Is Essential for a Successful Meiotic Program in the Mammalian Germline.

Mol Cell 2017 Oct 12;68(2):374-387.e12. Epub 2017 Oct 12.

Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland; European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.09.021DOI Listing
October 2017

Distinct Roles of RNA Helicases MVH and TDRD9 in PIWI Slicing-Triggered Mammalian piRNA Biogenesis and Function.

Dev Cell 2017 06;41(6):623-637.e9

Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2017.05.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5481186PMC
June 2017

PIWI Slicing and EXD1 Drive Biogenesis of Nuclear piRNAs from Cytosolic Targets of the Mouse piRNA Pathway.

Mol Cell 2016 Jan 6;61(1):138-52. Epub 2015 Dec 6.

European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.11.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4712191PMC
January 2016

Deep sequencing of mRNA in CD24(-) and CD24(+) mammary carcinoma Mvt1 cell line.

Genom Data 2015 Sep 9;5:399-401. Epub 2015 Jul 9.

Departments of Medicine, Endocrinology, Diabetes and Bone Disease, Icahn School of Medicine at Mount Sinai, NY 10029, United States.

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http://dx.doi.org/10.1016/j.gdata.2015.06.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583690PMC
September 2015

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire.

Genes Dev 2015 Aug;29(16):1747-62

Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria;

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http://dx.doi.org/10.1101/gad.267252.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561483PMC
August 2015

MIWI2 and MILI Have Differential Effects on piRNA Biogenesis and DNA Methylation.

Cell Rep 2015 Aug 13;12(8):1234-43. Epub 2015 Aug 13.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.07.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4554733PMC
August 2015

PIWI Slicing and RNA Elements in Precursors Instruct Directional Primary piRNA Biogenesis.

Cell Rep 2015 Jul 9;12(3):418-28. Epub 2015 Jul 9.

European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.06.030DOI Listing
July 2015

CD24(+) cells fuel rapid tumor growth and display high metastatic capacity.

Breast Cancer Res 2015 Jun 4;17:78. Epub 2015 Jun 4.

Diabetes and Metabolism Clinical Research Center of Excellence, Clinical Research Institute at Rambam (CRIR) and the Faculty of Medicine, Technion, Rambam Medical Center, P.O.B 9602, Haifa, 31096, Israel.

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http://dx.doi.org/10.1186/s13058-015-0589-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479226PMC
June 2015

Stable heteroplasmy at the single-cell level is facilitated by intercellular exchange of mtDNA.

Nucleic Acids Res 2015 Feb 4;43(4):2177-87. Epub 2015 Feb 4.

Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, NY 10029, USA

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http://dx.doi.org/10.1093/nar/gkv052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344500PMC
February 2015

Draft Genome Sequence of Bacillus alcalophilus AV1934, a Classic Alkaliphile Isolated from Human Feces in 1934.

Genome Announc 2014 Nov 13;2(6). Epub 2014 Nov 13.

Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, USA

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http://dx.doi.org/10.1128/genomeA.01175-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4241669PMC
November 2014

mRNA-Seq reveals novel molecular mechanisms and a robust fingerprint in Graves' disease.

J Clin Endocrinol Metab 2014 Oct 27;99(10):E2076-83. Epub 2014 Jun 27.

Thyroid Research Unit (X.Y., S.M., R.L., T.F.D.), Department of Medicine, and Departments of Oncological Science (R.Sa.) and Pathology (R.Sh.), Icahn School of Medicine at Mt Sinai and the James J. Peters Veterans Affairs Medical Center, New York, New York 10468.

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http://dx.doi.org/10.1210/jc.2014-1735DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184074PMC
October 2014

piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells.

Genes Dev 2014 Jul 17;28(13):1410-28. Epub 2014 Jun 17.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;

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http://dx.doi.org/10.1101/gad.240895.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083086PMC
July 2014

RNA clamping by Vasa assembles a piRNA amplifier complex on transposon transcripts.

Cell 2014 Jun 5;157(7):1698-711. Epub 2014 Jun 5.

European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.05.018DOI Listing
June 2014

Activating transcription factor 6 is necessary and sufficient for alcoholic fatty liver disease in zebrafish.

PLoS Genet 2014 29;10(5):e1004335. Epub 2014 May 29.

Department of Medicine - Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4038464PMC
December 2014

The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs.

RNA 2014 Jun 22;20(6):773-81. Epub 2014 Apr 22.

European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 38042 Grenoble, France.

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http://dx.doi.org/10.1261/rna.044701.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4024632PMC
June 2014

Global effects of the CSR-1 RNA interference pathway on the transcriptional landscape.

Nat Struct Mol Biol 2014 Apr 30;21(4):358-65. Epub 2014 Mar 30.

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.

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http://dx.doi.org/10.1038/nsmb.2801DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4068146PMC
April 2014

UHRF1 overexpression drives DNA hypomethylation and hepatocellular carcinoma.

Cancer Cell 2014 Feb 30;25(2):196-209. Epub 2014 Jan 30.

Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Liver Cancer Program/Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccr.2014.01.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951208PMC
February 2014

Multifaceted roles of miR-1s in repressing the fetal gene program in the heart.

Cell Res 2014 Mar 31;24(3):278-92. Epub 2014 Jan 31.

Mindich Child Health and Development Institute, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1040, New York, NY 10029, USA.

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http://dx.doi.org/10.1038/cr.2014.12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3945888PMC
March 2014

Tudor domain containing 12 (TDRD12) is essential for secondary PIWI interacting RNA biogenesis in mice.

Proc Natl Acad Sci U S A 2013 Oct 25;110(41):16492-7. Epub 2013 Sep 25.

European Molecular Biology Laboratory, Grenoble Outstation and Unit for Virus Host-Cell Interactions, Université Grenoble Alpes, European Molecular Biology Laboratory, Centre National de la Recherche Scientifique, 38042 Grenoble, France.

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http://dx.doi.org/10.1073/pnas.1316316110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799322PMC
October 2013

Bacterial argonaute samples the transcriptome to identify foreign DNA.

Mol Cell 2013 Sep;51(5):594-605

Division of Biology, California Institute of Technology, 147-75, 1200E California Boulevard, Pasadena, CA 91125, USA; Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square 2, Moscow 123182, Russia.

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http://dx.doi.org/10.1016/j.molcel.2013.08.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3809076PMC
September 2013

An in vivo RNAi screening approach to identify host determinants of virus replication.

Cell Host Microbe 2013 Sep;14(3):346-56

Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

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http://dx.doi.org/10.1016/j.chom.2013.08.007DOI Listing
September 2013

MiST: a new approach to variant detection in deep sequencing datasets.

Nucleic Acids Res 2013 Sep 4;41(16):e154. Epub 2013 Jul 4.

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, NY 10029, USA, The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, NY 10029, USA and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, NY 10029, USA.

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http://dx.doi.org/10.1093/nar/gkt551DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763541PMC
September 2013

A small-RNA enhancer of viral polymerase activity.

J Virol 2012 Dec 3;86(24):13475-85. Epub 2012 Oct 3.

Department of Microbiology, Mount Sinai School of Medicine, New York, New York, USA.

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http://dx.doi.org/10.1128/JVI.02295-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3503082PMC
December 2012

The cochaperone shutdown defines a group of biogenesis factors essential for all piRNA populations in Drosophila.

Mol Cell 2012 Sep 16;47(6):954-69. Epub 2012 Aug 16.

Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria.

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http://dx.doi.org/10.1016/j.molcel.2012.07.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463805PMC
September 2012

A TLR and non-TLR mediated innate response to lentiviruses restricts hepatocyte entry and can be ameliorated by pharmacological blockade.

Mol Ther 2012 Dec 7;20(12):2257-67. Epub 2012 Aug 7.

Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York City, NY 10028, USA.

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http://dx.doi.org/10.1038/mt.2012.150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3519984PMC
December 2012

Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing.

Nature 2011 Nov 27;480(7376):264-7. Epub 2011 Nov 27.

European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble, France.

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http://dx.doi.org/10.1038/nature10672DOI Listing
November 2011

Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing.

Nucleic Acids Res 2011 Nov 2;39(21):e141. Epub 2011 Sep 2.

Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA.

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http://dx.doi.org/10.1093/nar/gkr693DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3241666PMC
November 2011

Vreteno, a gonad-specific protein, is essential for germline development and primary piRNA biogenesis in Drosophila.

Development 2011 Sep 10;138(18):4039-50. Epub 2011 Aug 10.

HHMI and Kimmel Center for Biology and Medicine at Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.

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http://dx.doi.org/10.1242/dev.069187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160098PMC
September 2011

piRNA production requires heterochromatin formation in Drosophila.

Curr Biol 2011 Aug 4;21(16):1373-9. Epub 2011 Aug 4.

Department of Cell Biology, Howard Hughes Medical Institute and Kimmel Center for Biology and Medicine, Skirball Institute, New York University School of Medicine, New York, NY 10016, USA.

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http://dx.doi.org/10.1016/j.cub.2011.06.057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205116PMC
August 2011

Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells.

Curr Biol 2011 Mar 25;21(5):369-76. Epub 2011 Feb 25.

Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA.

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http://dx.doi.org/10.1016/j.cub.2011.01.067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088433PMC
March 2011

A growth-essential Tetrahymena Piwi protein carries tRNA fragment cargo.

Genes Dev 2010 Dec 24;24(24):2742-7. Epub 2010 Nov 24.

Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gad.1996210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3003190PMC
December 2010

Geoseq: a tool for dissecting deep-sequencing datasets.

BMC Bioinformatics 2010 Oct 12;11:506. Epub 2010 Oct 12.

Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA.

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http://dx.doi.org/10.1186/1471-2105-11-506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2972303PMC
October 2010

An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila.

EMBO J 2010 Oct 3;29(19):3301-17. Epub 2010 Sep 3.

Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.

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http://dx.doi.org/10.1038/emboj.2010.212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957214PMC
October 2010

Preference of RIG-I for short viral RNA molecules in infected cells revealed by next-generation sequencing.

Proc Natl Acad Sci U S A 2010 Sep 30;107(37):16303-8. Epub 2010 Aug 30.

Department of Microbiology, Mount Sinai School of Medicine, New York, NY 10029, USA.

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http://dx.doi.org/10.1073/pnas.1005077107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2941304PMC
September 2010

Mouse MOV10L1 associates with Piwi proteins and is an essential component of the Piwi-interacting RNA (piRNA) pathway.

Proc Natl Acad Sci U S A 2010 Jun 1;107(26):11841-6. Epub 2010 Jun 1.

Center for Animal Transgenesis and Germ Cell Research and Department of Animal Biology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1073/pnas.1003953107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2900664PMC
June 2010

Influenza A virus-generated small RNAs regulate the switch from transcription to replication.

Proc Natl Acad Sci U S A 2010 Jun 1;107(25):11525-30. Epub 2010 Jun 1.

Microbiology Graduate School Training Program, Department of Microbiology, Mount Sinai School of Medicine, New York, NY 10029, USA.

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http://dx.doi.org/10.1073/pnas.1001984107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895093PMC
June 2010

Sequence, biogenesis, and function of diverse small RNA classes bound to the Piwi family proteins of Tetrahymena thermophila.

Genes Dev 2009 Sep 5;23(17):2016-32. Epub 2009 Aug 5.

Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gad.1821209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2751968PMC
September 2009

Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform.

RNA 2009 Oct 27;15(10):1886-95. Epub 2009 Jul 27.

Harvard Medical School, Department of Genetics, Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1261/rna.1611309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743050PMC
October 2009

Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members.

Genes Dev 2009 Aug 7;23(15):1749-62. Epub 2009 Jul 7.

Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1101/gad.1814809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720255PMC
August 2009

An epigenetic role for maternally inherited piRNAs in transposon silencing.

Science 2008 Nov;322(5906):1387-92

Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory (CSHL), 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1126/science.1165171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805124PMC
November 2008

A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice.

Mol Cell 2008 Sep;31(6):785-99

Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1016/j.molcel.2008.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2730041PMC
September 2008

Genome analysis of the platypus reveals unique signatures of evolution.

Authors:
Wesley C Warren LaDeana W Hillier Jennifer A Marshall Graves Ewan Birney Chris P Ponting Frank Grützner Katherine Belov Webb Miller Laura Clarke Asif T Chinwalla Shiaw-Pyng Yang Andreas Heger Devin P Locke Pat Miethke Paul D Waters Frédéric Veyrunes Lucinda Fulton Bob Fulton Tina Graves John Wallis Xose S Puente Carlos López-Otín Gonzalo R Ordóñez Evan E Eichler Lin Chen Ze Cheng Janine E Deakin Amber Alsop Katherine Thompson Patrick Kirby Anthony T Papenfuss Matthew J Wakefield Tsviya Olender Doron Lancet Gavin A Huttley Arian F A Smit Andrew Pask Peter Temple-Smith Mark A Batzer Jerilyn A Walker Miriam K Konkel Robert S Harris Camilla M Whittington Emily S W Wong Neil J Gemmell Emmanuel Buschiazzo Iris M Vargas Jentzsch Angelika Merkel Juergen Schmitz Anja Zemann Gennady Churakov Jan Ole Kriegs Juergen Brosius Elizabeth P Murchison Ravi Sachidanandam Carly Smith Gregory J Hannon Enkhjargal Tsend-Ayush Daniel McMillan Rosalind Attenborough Willem Rens Malcolm Ferguson-Smith Christophe M Lefèvre Julie A Sharp Kevin R Nicholas David A Ray Michael Kube Richard Reinhardt Thomas H Pringle James Taylor Russell C Jones Brett Nixon Jean-Louis Dacheux Hitoshi Niwa Yoko Sekita Xiaoqiu Huang Alexander Stark Pouya Kheradpour Manolis Kellis Paul Flicek Yuan Chen Caleb Webber Ross Hardison Joanne Nelson Kym Hallsworth-Pepin Kim Delehaunty Chris Markovic Pat Minx Yucheng Feng Colin Kremitzki Makedonka Mitreva Jarret Glasscock Todd Wylie Patricia Wohldmann Prathapan Thiru Michael N Nhan Craig S Pohl Scott M Smith Shunfeng Hou Mikhail Nefedov Pieter J de Jong Marilyn B Renfree Elaine R Mardis Richard K Wilson

Nature 2008 May;453(7192):175-83

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature06936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803040PMC
May 2008

An endogenous small interfering RNA pathway in Drosophila.

Nature 2008 Jun 7;453(7196):798-802. Epub 2008 May 7.

Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1038/nature07007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895258PMC
June 2008

Conservation of small RNA pathways in platypus.

Genome Res 2008 Jun 7;18(6):995-1004. Epub 2008 May 7.

Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1101/gr.073056.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2413167PMC
June 2008

RNAi: design and analysis.

Curr Protoc Bioinformatics 2004 Sep;Chapter 12:Unit 12.3

Sachidanandam Lab, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

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http://dx.doi.org/10.1002/0471250953.bi1203s6DOI Listing
September 2004

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes.

Nature 2008 May 10;453(7194):534-8. Epub 2008 Apr 10.

Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1038/nature06904DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981145PMC
May 2008

A role for microRNAs in maintenance of mouse mammary epithelial progenitor cells.

Genes Dev 2007 Dec;21(24):3238-43

Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1101/gad.1616307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2113025PMC
December 2007

Developmentally regulated piRNA clusters implicate MILI in transposon control.

Science 2007 May 19;316(5825):744-7. Epub 2007 Apr 19.

Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Howard Hughes Medical Institute (HHMI), 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1126/science.1142612DOI Listing
May 2007

Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila.

Cell 2007 Mar 8;128(6):1089-103. Epub 2007 Mar 8.

Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1016/j.cell.2007.01.043DOI Listing
March 2007

Comprehensive splice-site analysis using comparative genomics.

Nucleic Acids Res 2006 12;34(14):3955-67. Epub 2006 Aug 12.

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1093/nar/gkl556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557818PMC
September 2006

A germline-specific class of small RNAs binds mammalian Piwi proteins.

Nature 2006 Jul 4;442(7099):199-202. Epub 2006 Jun 4.

Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1038/nature04917DOI Listing
July 2006

Short/branched-chain acyl-CoA dehydrogenase deficiency due to an IVS3+3A>G mutation that causes exon skipping.

Hum Genet 2006 Feb 30;118(6):680-90. Epub 2005 Nov 30.

Research Unit for Molecular Medicine, Aarhus University Hospital and Faculty of Health Science, Skejby Sygehus, Aarhus, Denmark.

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http://dx.doi.org/10.1007/s00439-005-0070-4DOI Listing
February 2006

Second-generation shRNA libraries covering the mouse and human genomes.

Nat Genet 2005 Nov 2;37(11):1281-8. Epub 2005 Oct 2.

Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1038/ng1650DOI Listing
November 2005

GeneSeer: a sage for gene names and genomic resources.

BMC Genomics 2005 Sep 21;6:134. Epub 2005 Sep 21.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

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http://dx.doi.org/10.1186/1471-2164-6-134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1266031PMC
September 2005

Cloning of short hairpin RNAs for gene knockdown in mammalian cells.

Nat Methods 2004 Nov;1(2):163-7

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1038/nmeth1104-163DOI Listing
November 2004

GObar: a gene ontology based analysis and visualization tool for gene sets.

BMC Bioinformatics 2005 Jul 25;6:189. Epub 2005 Jul 25.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

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http://dx.doi.org/10.1186/1471-2105-6-189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1190157PMC
July 2005

RNAi as a bioinformatics consumer.

Brief Bioinform 2005 Jun;6(2):146-62

Cold Spring Harbor Laboratory, NY 11724, USA.

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http://dx.doi.org/10.1093/bib/6.2.146DOI Listing
June 2005

Determinants of the inherent strength of human 5' splice sites.

RNA 2005 May;11(5):683-98

Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1261/rna.2040605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370755PMC
May 2005

Short hairpin activated gene silencing in mammalian cells.

Methods Mol Biol 2004 ;265:85-100

Cold Spring Harbor Laboratory, Watson School of Biological Sciences, Cold Spring Harbor, NY, USA.

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http://dx.doi.org/10.1385/1-59259-775-0:085DOI Listing
July 2004

Free energy lights the path toward more effective RNAi.

Nat Genet 2003 Dec;35(4):303-5

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http://dx.doi.org/10.1038/ng1203-303DOI Listing
December 2003