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44 Article(s) on File
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Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing
Le Thomas A,
Stuwe E,
Li S,
Du J,
Marinov G,
Rozhkov N,
Chen YC,
Luo Y,
Sachidanandam R,
Toth KF,
Patel D,
Aravin AA

Genes Development
  28 (15): 1667-80; Aug 1 2014   Nlm
[Abstract]
[DOI] [Full Text]

Vreteno, a gonad-specific protein, is essential for germline development and primary piRNA biogenesis in Drosophila
Zamparini AL,
Davis MY,
Malone CD,
Vieira E,
Zavadil J,
Sachidanandam R,
Hannon GJ,
Lehmann R

Development
  138 (18): 4039-4050; Sep 15 2011   PMC3160098
[Abstract]
[DOI]

piRNA Production Requires Heterochromatin Formation in Drosophila
Rangan P,
Malone CD,
Navarro C,
Newbold SP,
Hayes PS,
Sachidanandam R,
Hannon GJ,
Lehmann R

Current Biology
  21 (16): 1373-1379; Aug 23 2011   PMC3205116
[Abstract]
[DOI] [Full Text]

Tudor domain containing 7 (Tdrd7) is essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis
Tanaka T,
Hosokawa M,
Vagin VV,
Reuter M,
Hayashi E,
Mochizuki AL,
Kitamura K,
Yamanaka H,
Kondoh G,
Okawa K,
Kuramochi-Miyagawa S,
Nakano T,
Sachidanandam R,
Hannon GJ,
Pillai RS,
Nakatsuji N,
Chuma S

Proceedings of the National Academy of Sciences of the United States of America
  108 (26): 10579-10584; Jun 2011   PMC3127926
[Abstract]
[DOI]

Small RNA-based silencing strategies for transposons in the process of invading Drosophila species
Rozhkov NV,
Aravin AA,
Zelentsova ES,
Schostak NG,
Sachidanandam R,
McCombie WR,
Hannon GJ,
Evgenev MB

RNA
  16 (8): 1634-1645; Aug 2010   PMCID: PMC2905761
[Abstract]
[DOI] [Full Text] [PDF]

The RNA interference system differently responds to the same mobile element in distant Drosophila species
Rozhkov NV,
Aravin AA,
Sachidanandam R,
Hannon GJ,
Sokolova ON,
Zelentsova ES,
Shostak NG,
Evgenev MB

Doklady Biochemistry and Biophysics
  431 (1): 79-81; Apr 18 2010   PMCID: PMC2998894
[DOI] [Full Text] [PDF]

Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform
Zhou R,
Czech B,
Brennecke J,
Sachidanandam R,
Wohlschlegel JA,
Perrimon N,
Hannon GJ

RNA
  15 (10): 1886-1895; Oct 2009   PMCID: PMC2743050
[Abstract]
[DOI] [Full Text] [PDF]

Sequence, biogenesis, and function of diverse small RNA classes bound to the Piwi family proteins of Tetrahymena thermophila
Couvillion MT,
Lee SR,
Hogstad B,
Malone CD,
Tonkin LA,
Sachidanandam R,
Hannon GJ,
Collins K

Genes Dev
  23 (17): 2016-32; Sep 1 2009   PMCID: PMC2751968
[Abstract]
[DOI] [Full Text] [PDF]

Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members
Vagin VV,
Wohlschlegel J,
Qu J,
Jonsson Z,
Huang X,
Chuma S,
Girard A,
Sachidanandam R,
Hannon GJ,
Aravin AA

Genes Dev
  23 (15): 1749-62; Aug 1 2009   PMCID: PMC2720255
[Abstract]
[DOI] [Full Text] [PDF]

Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary
Malone CD,
Brennecke J,
Dus M,
Stark A,
McCombie WR,
Sachidanandam R,
Hannon GJ

Cell
  137 (3): 522-535 ; May 1 2009  
[Abstract]
[DOI] [Full Text] [PDF]

Post-transcriptional processing generates a diversity of 5-modified long and short RNAs
Fejes-Toth K,
Sotirova V,
Sachidanandam R,
Assaf G,
Hannon GJ,
Kapranov P,
Foissac S,
Willingham AT,
Duttagupta R,
Dumais E,
Gingeras TR

Nature
  457 (7232): 1028-1032; Feb 2009   PMCID: PMC2719882
[Abstract]
[DOI] [Full Text] [PDF]

An epigenetic role for maternally inherited piRNAs in transposon silencing
Brennecke J,
Malone CD,
Aravin AA,
Sachidanandam R,
Stark A,
Hannon GJ

Science
  322 (5906): 1387-92; Nov 28 2008  
[Abstract]
[DOI] [Full Text] [PDF]

Microrna 16 Regulates Expression of the Human 5-Aminolevulinic Acid Synthase-1 (Alas 1) Gene through Targeting the Coding Region of the Gene
Zheng JY,
Sachidanandam R,
Bennett K,
Bonkovsky HL

Hepatology
  48 (4): 1117A; Oct 2008  


A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice
Aravin AA,
Sachidanandam R,
Bourchis D,
Schaefer C,
Pezic D,
Fejes Toth K,
Bestor T,
Hannon GJ

Mol Cell
  31 (6): 785-99; Sep 26 2008  
[Abstract]
[DOI] [Full Text] [PDF]

Kismeth: analyzer of plant methylation states through bisulfite sequencing
Gruntman E,
Qi Y,
Slotkin RK,
Roeder T,
Martienssen RA,
Sachidanandam R

BMC bioinformatics
  9 (0): 371; Sep 11 2008  
[Abstract]
[DOI] [Full Text]

Conservation of small RNA pathways in platypus
Murchison EP,
Kheradpour P,
Sachidanandam R,
Smith C,
Hodges E,
Xuan Z,
Kellis M,
Grutzner F,
Stark A,
Hannon GJ

Genome Res
  18 (6): 995-1004; Jun 2008  
[Abstract]
[DOI] [Full Text] [PDF]

An endogenous small interfering RNA pathway in Drosophila
Czech B,
Malone CD,
Zhou R,
Stark A,
Schlingeheyde C,
Dus M,
Perrimon N,
Kellis M,
Wohlschlegel JA,
Sachidanandam R,
Hannon GJ,
Brennecke J

Nature
  453 (7196): 798-802; Jun 2008  
[Abstract]
[DOI] [Full Text] [PDF]

Genome analysis of the platypus reveals unique signatures of evolution
Warren WC,
Hillier LW,
Marshall Graves JA,
Birney E,
Ponting CP,
Grutzner F,
Belov K,
Miller W,
Clarke L,
Chinwalla AT,
Yang SP,
Heger A,
Locke DP,
Miethke P,
Waters PD,
Veyrunes F,
Fulton L,
Fulton B,
Graves T,
Wallis J,
Puente XS,
Lopez-Otin C,
Ordonez GR,
Eichler EE,
Chen L,
Cheng Z,
Deakin JE,
Alsop A,
Thompson K,
Kirby P,
Papenfuss AT,
Wakefield MJ,
Olender T,
Lancet D,
Huttley GA,
Smit AF,
Pask A,
Temple-Smith P,
Batzer MA,
Walker JA,
Konkel MK,
Harris RS,
Whittington CM,
Wong ES,
Gemmell NJ,
Buschiazzo E,
Vargas Jentzsch IM,
Merkel A,
Schmitz J,
Zemann A,
Churakov G,
Kriegs JO,
Brosius J,
Murchison EP,
Sachidanandam R,
Smith C,
Hannon GJ,
Tsend-Ayush E,
McMillan D,
Attenborough R,
Rens W,
Ferguson-Smith M,
Lefevre CM,
Sharp JA,
Nicholas KR,
Ray DA,
Kube M,
Reinhardt R,
Pringle TH,
Taylor J,
Jones RC,
Nixon B,
Dacheux JL,
Niwa H,
Sekita Y,
Huang X,
Stark A,
Kheradpour P,
Kellis M,
Flicek P,
Chen Y,
Webber C,
Hardison R,
Nelson J,
Hallsworth-Pepin K,
Delehaunty K,
Markovic C,
Minx P,
Feng Y,
Kremitzki C,
Mitreva M,
Glasscock J,
Wylie T,
Wohldmann P,
Thiru P,
Nhan MN,
Pohl CS,
Smith SM,
Hou S,
Renfree MB,
Mardis ER,
Wilson RK

Nature
  453 (7192): 175-83; May 8 2008   PMC2803040
[Abstract]
[DOI] [Full Text] [PDF]

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes
Tam OH,
Aravin AA,
Stein P,
Girard A,
Murchison EP,
Cheloufi S,
Hodges E,
Anger M,
Sachidanandam R,
Schultz RM,
Hannon GJ

Nature
  453 (0): 534-538 ; May 22 2008   PMC2981145
[Abstract]
[DOI] [Full Text] [PDF]

Features of 5-splice-site efficiency derived from disease-causing mutations and comparative genomics
Roca X,
Olson AJ,
Rao AR,
Enerly E,
Kristensen VN,
Borresen-Dale AL,
Andresen BS,
Krainer AR,
Sachidanandam R

Genome Res
  18 (1): 77-87; Jan 2008   PMCID: PMC2134769
[Abstract]
[DOI] [Full Text] [PDF]

Analysis of large-scale sequencing of small RNAs
Olson AJ,
Brennecke J,
Aravin AA,
Hannon GJ,
Sachidanandam R

Pac Symp Biocomput
  13 (0): 126-36; 2008  
[Abstract]
[Full Text] [PDF]

A role for microRNAs in maintenance of mouse mammary epithelial progenitor cells
Ibarra I,
Erlich Y,
Muthuswamy SK,
Sachidanandam R,
Hannon GJ

Genes Dev
  21 (24): 3238-43; Dec 15 2007   PMCID: PMC2113025
[Abstract]
[DOI] [Full Text] [PDF]

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context
Faith JJ,
Olson AJ,
Gardner TS,
Sachidanandam R

Bmc Bioinformatics
  8 (0): 344; Sep 2007   PMCID: PMC2238324
[DOI] [Full Text] [PDF]

Developmentally regulated piRNA clusters implicate MILI in transposon control
Aravin AA,
Sachidanandam R,
Girard A,
Fejes-Toth K,
Hannon GJ

Science
  316 (5825): 744-7; May 4 2007  
[Abstract]
[DOI] [Full Text] [PDF]

Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila
Brennecke J,
Aravin AA,
Stark A,
Dus M,
Kellis M,
Sachidanandam R,
Hannon GJ

Cell
  128 (6): 1089-103; Mar 23 2007  
[Abstract]
[DOI] [Full Text] [PDF]

Second-generation shRNA libraries covering the mouse and human genomes
Silva JM,
Li MZ,
Chang K,
Ge W,
Golding MC,
Rickles RJ,
Siolas D,
Hu G,
Paddison PJ,
Schlabach MR,
Sheth N,
Bradshaw J,
Burchard J,
Kulkarni A,
Cavet G,
Sachidanandam R,
McCombie WR,
Cleary MA,
Elledge SJ,
Hannon GJ

Nat Genet
  37 (11): 1281-8; Nov 2005  
[Abstract]
[DOI] [Full Text]

High-density single-nucleotide polymorphism maps of the human genome
Miller RD,
Phillips MS,
Jo I,
Donaldson MA,
Studebaker JF,
Addleman N,
Alfisi SV,
Ankener WM,
Bhatti HA,
Callahan CE,
Carey BJ,
Conley CL,
Cyr JM,
Derohannessian V,
Donaldson RA,
Elosua C,
Ford SE,
Forman AM,
Gelfand CA,
Grecco NM,
Gutendorf SM,
Hock CR,
Hozza MJ,
Hur S,
In SM,
Jackson DL,
Jo SA,
Jung SC,
Kim S,
Kimm K,
Kloss EF,
Koboldt DC,
Kuebler JM,
Kuo FS,
Lathrop JA,
Lee JK,
Leis KL,
Livingston SA,
Lovins EG,
Lundy ML,
Maggan S,
Minton M,
Mockler MA,
Morris DW,
Nachtman EP,
Oh B,
Park C,
Park CW,
Pavelka N,
Perkins AB,
Restine SL,
Sachidanandam R,
Reinhart AJ,
Scott KE,
Shah GJ,
Tate JM,
Varde SA,
Walters A,
White JR

Genomics
  86 (2): 117-126; Aug 2005  
[Abstract]
[Full Text]

Rnai codex - a comprehensive RNAi resource
Olson A,
Sheth N,
Lee J,
Hannon GJ,
Sachidanandam R

Briefings in Bioinformatics
  6 (1): 104-106; Mar 2005  
[Full Text]

Cloning of short hairpin RNAs for gene knockdown in mammalian cells
Paddison PJ,
Cleary M,
Silva JM,
Chang K,
Sheth N,
Sachidanandam R,
Hannon GJ

Nat Methods
  1 (2): 163-7; Nov 2004  
[DOI] [Full Text]

RNAi: design and analysis
Sachidanandam R

Curr Protoc Bioinformatics
  Chapt (0): Unit 12.3; Sep 2004  
[Abstract]
[DOI] [Full Text] [PDF]

A resource for large-scale RNA-interference-based screens in mammals
Paddison PJ,
Silva JM,
Conklin DS,
Schlabach M,
Li M,
Aruleba S,
Balija V,
OShaughnessy A,
Gnoj L,
Scobie K,
Chang K,
Westbrook T,
Cleary M,
Sachidanandam R,
McCombie WR,
Elledge SJ,
Hannon GJ

Nature
  428 (6981): 427-31; Mar 25 2004  
[Abstract]
[DOI] [Full Text]

From silencing to gene expression: real-time analysis in single cells
Janicki SM,
Tsukamoto T,
Salghetti SE,
Tansey WP,
Sachidanandam R,
Prasanth KV,
Ried T,
Shav-Tal Y,
Bertrand E,
Singer RH,
Spector DL

Cell
  116 (5): 683-98; Mar 5 2004  
[Abstract]
[DOI] [Full Text] [PDF]

Short hairpin activated gene silencing in mammalian cells
Paddison PJ,
Caudy AA,
Sachidanandam R,
Hannon GJ
In:
RNA Interference, Editing and Modification: methods and protocols
(ed. Gott, J. M. ) Totowa, N. J. : Humana Press; 2004. 265: 85-100  
[Abstract]
[Full Text]

Free energy lights the path toward more effective RNAi
Silva JM,
Sachidanandam R,
Hannon GJ

Nature Genetics
  35 (4): 303-305; Dec 2003  
[Abstract]
[Full Text]

Intrinsic differences between authentic and cryptic 5 splice sites
Roca X,
Sachidanandam R,
Krainer AR

Nucleic Acids Research
  31 (21): 6321-6333; Nov 2003  
[Abstract]
[Full Text]

A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set
Matise TC,
Sachidanandam R,
Clark AG,
Kruglyak L,
Wijsman E,
Kakol J,
Buyske S,
Chui B,
Cohen P,
de Toma C,
Ehm M,
Glanowski S,
He CS,
Heil J,
Markianos K,
McMullen I,
Pericak-Vance MA,
Silbergleit A,
Stein L,
Wagner M,
Wilson AF,
Winick JD,
Winn-Deen ES,
Yamashiro CT,
Cann HM,
Lai E,
Holden AL

American Journal of Human Genetics
  73 (2): 271-284; Aug 2003  
[Abstract]
[Full Text]

Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots
Phillips MS,
Lawrence R,
Sachidanandam R,
Morris AP,
Balding DJ,
Donaldson MA,
Studebaker JF,
Ankener WM,
Alfisi SV,
Kuo FS,
Camisa AL,
Pazorov V,
Scott KE,
Carey BJ,
Faith J,
Katari G,
Bhatti HA,
Cyr JM,
Derohannessian V,
Elosua C,
Forman AM,
Grecco NM,
Hock CR,
Kuebler JM,
Lathrop JA,
Mockler MA,
Nachtman EP,
Restine SL,
Varde SA,
Hozza MJ,
Gelfand CA,
Broxholme J,
Abecasis GR,
Boyce-Jacino MT,
Cardon LR

Nature Genetics
  33 (3): 382-387; Mar 2003  
[Abstract]
[Full Text]

Single-molecule observations of DNA denaturation: mechanical and enzymatic effects
Strick TR,
Sachidanandam R,
Revyakin A,
Ebright RH

Biophysical Journal
  84 (2): 309A-309A; Feb 2003  
[Full Text]

A first generation haplotype map of chromosome 19
Boyce-Jacino MT,
Sachidanandam R,
Donaldson MA,
Abecasis GR,
Lawrence R,
Studebaker JF,
Ankener WM,
Kuo FS,
Alfisi SV,
Gelfand CA,
Phillips M,
Cardon LR

American Journal of Human Genetics
  71 (4): 205-205; Oct 2002  
[Full Text]

A haplotype map of chromosome 19
Boyce-Jacino MT,
Sachidanandam R,
Donaldson MA,
Abecasis GR,
Lawrence R,
Studebaker JF,
Ankener WM,
Kuo FS,
Alfisi SV,
Gelfand CA,
Phillips M,
Cardon LR

American Journal of Human Genetics
  71 (4): 205-205; Oct 2002  
[Full Text]

A high-resolution human SNP linkage map
Matise TC,
Sachidanandam R,
Clark A,
Kruglyak L,
Wijsman E,
Chui B,
Cohen P,
de Toma C,
Ehm M,
Glanowski S,
He C,
Heil J,
McMullen I,
Stein L,
Wagner M,
Winick J,
Winn-Deen ES,
Cann HM,
Lai E,
Holden HL

American Journal of Human Genetics
  71 (4): 206-206; Oct 2002  
[Full Text]

Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order
Liu H,
Sachidanandam R,
Stein L

Genome Research
  11 (12): 2020-2026; Dec 2001  
[Abstract]
[DOI] [Full Text]

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
Sachidanandam R,
Weissman D,
Schmidt SC,
Kakol JM,
Stein LD,
Marth G,
Sherry S,
Mullikin JC,
Mortimore BJ,
Willey DL,
Hunt SE,
Cole CG,
Coggill PC,
Rice CM,
Ning Z,
Rogers J,
Bentley DR,
Kwok PY,
Mardis ER,
Yeh RT,
Schultz B,
Cook L,
Davenport R,
Dante M,
Fulton L,
Hillier L,
Waterston RH,
McPherson JD,
Gilman B,
Schaffner S,
Van Etten WJ,
Reich D,
Higgins J,
Daly MJ,
Blumenstiel B,
Baldwin J,
Stange-Thomann N,
Zody MC,
Linton L,
Lander ES,
Altshuler D

Nature
  409 (6822): 928-33; Feb 15 2001  
[Abstract]
[Full Text]

A high-resolution radiation hybrid map of the human genome draft sequence
Olivier M,
Aggarwal A,
Allen J,
Almendras AA,
Bajorek ES,
Beasley EM,
Brady SD,
Bushard JM,
Bustos VI,
Chu A,
Chung TR,
De Witte A,
Denys ME,
Dominguez R,
Fang NY,
Foster BD,
Freudenberg RW,
Hadley D,
Hamilton LR,
Jeffrey TJ,
Kelly L,
Lazzeroni L,
Levy MR,
Lewis SC,
Liu X,
Lopez FJ,
Louie B,
Marquis JP,
Martinez RA,
Matsuura MK,
Misherghi NS,
Norton JA,
Olshen A,
Perkins SM,
Perou AJ,
Piercy C,
Piercy M,
Qin F,
Reif T,
Sheppard K,
Shokoohi V,
Smick GA,
Sun WL,
Stewart EA,
Tejeda JF,
Tran NM,
Trejo T,
Vo NT,
Yan SC,
Zierten DL,
Zhao SY,
Sachidanandam R,
Trask BJ,
Myers RM,
Cox DR

Science
  291 (5507): 1298-+; Feb 2001  
[Abstract]
[Full Text]


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