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microRNA100 inhibits self-renewal of breast cancer stem-like cells and breast tumor development
Deng L,
Shang L,
Bai S,
Chen J,
He X,
Trevino RM,
Chen S,
Li X,
Meng X,
Yu B,
Wang X,
Liu Y,
McDermott SP,
Ariazi AE,
Ginestier C,
Ibarra I,
Ke J,
Luther TK,
Clouthier SG,
Xu L,
Shan G,
Song E,
Yao H,
Hannon GJ,
Weiss SJ,
Wicha MS,
Liu S

Cancer Research
  74 (22): 6648-6660; Nov 15 2014   Nlm
[Abstract]
[DOI] [Full Text]

Inflammation-Induced NFATc1-STAT3 Transcription Complex Promotes Pancreatic Cancer Initiation by Kras(G12D)
Baumgart S,
Chen NM,
Siveke JT,
Konig A,
Zhang JS,
Singh SK,
Wolf E,
Bartkuhn M,
Esposito I,
Hessmann E,
Reinecke J,
Nikorowitsch J,
Brunner M,
Singh G,
Fernandez-Zapico ME,
Smyrk T,
Bamlet WR,
Eilers M,
Neesse A,
Gress TM,
Billadeau DD,
Tuveson D,
Urrutia R,
Ellenrieder V

Cancer Discovery
  4 (6): 688-701; Jun 2014   NLM
[Abstract]
[DOI] [Full Text]

A promoter-level mammalian expression atlas
Forest AR,
Kawaji H,
Rehli M,
Baillie JK,
De Hoon MJ,
Haberle V,
Lassmann T,
Kulakovskiy IV,
Lizio M,
Itoh M,
Andersson R,
Mungall CJ,
Meehan TF,
Schmeier S,
Bertin N,
Jørgensen M,
Dimont E,
Arner E,
Schmidl C,
Schaefer U,
Medvedeva YA,
Plessy C,
Vitezic M,
Severin J,
Semple CA,
Ishizu Y,
Young RS,
Francescatto M,
Altschuler IA,
Albanese D,
Altschule GM,
Arakawa T,
Archer JA,
Arner P,
Babina M,
Rennie S,
Balwierz PJ,
Beckhouse AG,
Pradhan-Bhatt S,
Blake JA,
Blumenthal A,
Bodega B,
Bonetti A,
Briggs J,
Brombacher F,
Burroughs AM,
Califano A,
Cannistraci CV,
Carbajo D,
Chen Y,
Chierici M,
Ciani Y,
Clevers HC,
Dalla E,
Davis CA,
Detmar M,
Diehl AD,
Dohi T,
Drabløs F,
Edge AS,
Edinger M,
Ekwall K,
Endoh M,
Enomoto H,
Fagiolini M,
Fairbairn L,
Fang H,
Farach-Carson MC,
Faulkner GJ,
Favorov AV,
Fisher ME,
Frith MC,
Fujita R,
Fukuda S,
Furlanello C,
Furuno M,
Furusawa JI,
Geijtenbeek TB,
Gibson AP,
Gingeras T,
Goldowitz D,
Gough J,
Guhl S,
Guler R,
Gustincich S,
Ha TJ,
Hamaguchi M,
Hara M,
Harbers M,
Harshbarger J,
Hasegawa A,
Hasegawa Y,
Hashimoto T,
Herlyn M,
Hitchens KJ,
Sui SJ,
Hofmann OM,
Hoof I,
Hori F,
Huminiecki L,
Iida K,
Ikawa T,
Jankovic BR,
Jia H,
Joshi A,
Jurman G,
Kaczkowski B,
Kai C,
Kaida K,
Kaiho A,
Kajiyama K,
Kanamori-Katayama M,
Kasianov AS,
Kasukawa T,
Katayama S,
Kato S,
Kawaguchi S,
Kawamoto H,
Kawamura YI,
Kawashima T,
Kempfle JS,
Kenna TJ,
Kere J,
Khachigian LM,
Kitamura T,
Klinken SP,
Knox AJ,
Kojima M,
Kojima S,
Kondo N,
Koseki H,
Koyasu S,
Krampitz S,
Kubosaki A,
Kwon AT,
Laros JF,
Lee W,
Lennartsson A,
Li K,
Lilje B,
Lipovich L,
Mackay-sim A,
Manabe RI,
Mar JC,
Marchand B,
Mathelier A,
Mejhert N,
Meynert A,
Mizuno Y,
De Morais DA,
Morikawa H,
Morimoto M,
Moro K,
Motakis E,
Motohashi H,
Mummery CL,
Murata M,
Nagao-Sato S,
Nakachi Y,
Nakahara F,
Nakamura T,
Nakamura Y,
Nakazato K,
Van Nimwegen E,
Ninomiya N,
Nishiyori H,
Noma S,
Nozaki T,
Ogishima S,
Ohkura N,
Ohmiya H,
Ohno H,
Ohshima M,
Okada-Hatakeyama M,
Okazaki Y,
Orlando V,
Ovchinnikov DA,
Pain A,
Passier R,
Patrikakis M,
Persson H,
Piazza S,
Prendergast JG,
Rackham OJ,
Ramilowski JA,
Rashid M,
Ravasi T,
Rizzu P,
Roncador M,
Roy S,
Rye MB,
Saijyo E,
Sajantila A,
Saka A,
Sakaguchi S,
Sakai M,
Sato H,
Satoh H,
Savvi S,
Saxena A,
Schneider C,
Schultes EA,
Schulze-Tanzil GG,
Schwegmann A,
Sengstag T,
Sheng G,
Shimoji H,
Shimoni Y,
Shin JW,
Simon C,
Sugiyama D,
Sugiyama T,
Suzuki M,
Suzuki N,
Swoboda RK,
T Hoen PA,
Tagami M,
Tagami NT,
Takai J,
Tanaka H,
Tatsukawa H,
Tatum Z,
Thompson M,
Toyoda H,
Toyoda T,
Valen E,
Van De Wetering M,
Van Den Berg LM,
Verardo R,
Vijayan D,
Vorontsov IE,
Wasserman WW,
Watanabe S,
Wells CA,
Winteringham LN,
Wolvetang E,
Wood EJ,
Yamaguchi Y,
Yamamoto M,
Yoneda M,
Yonekura Y,
Yoshida S,
Zabierowski SE,
Zhang PG,
Zhao X,
Zucchelli S,
Summers KM,
Suzuki H,
Daub CO,
Kawai J,
Heutink P,
Hide W,
Freeman TC,
Lenhard B,
Bajic LV,
Taylor MS,
Makeev VJ,
Sandelin A,
Hume DA,
Carninci P,
Hayashizaki Y

Nature
  507 (7493): 462-470; Mar 27 2014   NLM
[DOI] [Full Text]

An integrated encyclopedia of DNA elements in the human genome
Dunham I,
Kundaje A,
Aldred SF,
Collins PJ,
Davis C,
Doyle F,
Epstein CB,
Frietze S,
Harrow J,
Kaul R,
Khatun J,
Lajoie BR,
Landt SG,
Lee BK,
Pauli F,
Rosenbloom KR,
Sabo P,
Safi A,
Sanyal A,
Shoresh N,
Simon JM,
Song L,
Trinklein ND,
Altshuler RC,
Birney E,
Brown JB,
Cheng C,
Djebali S,
Dong XJ,
Ernst J,
Furey TS,
Gerstein M,
Giardine B,
Greven M,
Hardison RC,
Harris RS,
Herrero J,
Hoffman MM,
Iyer S,
Kellis M,
Kheradpour P,
Lassmann T,
Li QH,
Lin X,
Marinov GK,
Merkel A,
Mortazavi A,
Parker SC,
Reddy TE,
Rozowsky J,
Schlesinger F,
Thurman RE,
Wang J,
Ward LD,
Whitfield TW,
Wilder SP,
Wu W,
Xi HL,
Yip KY,
Zhuang JL,
Bernstein BE,
Green ED,
Gunter C,
Snyder M,
Pazin MJ,
Lowdon RF,
Dillon LA,
Adams LB,
Kelly CJ,
Zhang J,
Wexler JR,
Good PJ,
Feingold EA,
Crawford GE,
Dekker J,
Elnitski L,
Farnham PJ,
Giddings MC,
Gingeras TR,
Guigo R,
Hubbard TJ,
Kent WJ,
Lieb JD,
Margulies EH,
Myers RM,
Stamatoyannopoulos JA,
Tenenbaum SA,
Weng ZP,
White KP,
Wold B,
Yu Y,
Wrobel J,
Risk BA,
Gunawardena HP,
Kuiper HC,
Maier CW,
Xie L,
Chen X,
Mikkelsen TS,
Gillespie S,
Goren A,
Ram O,
Zhang XL,
Wang L,
Issner R,
Coyne MJ,
Durham T,
Ku M,
Truong T,
Eaton ML,
Davis CA,
Dobin A,
Tanzer A,
Lagarde J,
Lin W,
Xue CH,
Williams BA,
Zaleski C,
Roeder M,
Kokocinski F,
Abdelhamid RF,
Alioto T,
Antoshechkin I,
Baer MT,
Batut P,
Bell I,
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Chakrabortty S,
Chrast J,
Curado J,
Derrien T,
Drenkow J,
Dumais E,
Dumais J,
Duttagupta R,
Fastuca M,
Fejes-Toth K,
Ferreira P,
Foissac S,
Fullwood MJ,
Gao H,
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Gordon A,
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Jha S,
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King B,
Kingswood C,
Li GL,
Luo OJ,
Park E,
Preall JB,
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Ribeca P,
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Ruan XA,
Sammeth M,
Sandhu KS,
Schaeffer L,
See LH,
Shahab A,
Skancke J,
Suzuki AM,
Takahashi H,
Tilgner H,
Trout D,
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Wang HE,
Yu YB,
Hayashizaki Y,
Reymond A,
Antonarakis SE,
Hannon GJ,
Ruan YJ,
Carninci P,
Sloan CA,
Learned K,
Malladi VS,
Wong MC,
Barber G,
Cline MS,
Dreszer TR,
Heitner SG,
Karolchik D,
Kirkup VM,
Meyer LR,
Long JC,
Maddren M,
Raney BJ,
Song LY,
Grasfeder LL,
Giresi PG,
Battenhouse A,
Sheffield NC,
Showers KA,
London D,
Bhinge AA,
Shestak C,
Schaner MR,
Kim SK,
Zhang ZZ,
Mieczkowski PA,
Mieczkowska JO,
Liu Z,
McDaniell RM,
Ni YY,
Rashid NU,
Kim MJ,
Adar S,
Zhang ZC,
Wang TY,
Winter D,
Keefe D,
Iyer VR,
Zheng MZ,
Wang P,
Gertz J,
Vielmetter J,
Partridge EC,
Varley KE,
Gasper C,
Bansal A,
Pepke S,
Jain P,
Amrhein H,
Bowling KM,
Anaya M,
Cross MK,
Muratet MA,
Newberry KM,
McCue K,
Nesmith AS,
Fisher-Aylor KI,
Pusey B,
DeSalvo G,
Parker SL,
Balasubramanian S,
Davis NS,
Meadows SK,
Eggleston T,
Newberry JS,
Levy SE,
Absher DM,
Wong WH,
Blow MJ,
Visel A,
Pennachio LA,
Petrykowska HM,
Abyzov A,
Aken B,
Barrell D,
Barson G,
Berry A,
Bignell A,
Boychenko V,
Bussotti G,
Davidson C,
Despacio-Reyes G,
Diekhans M,
Ezkurdia I,
Frankish A,
Gilbert J,
Gonzalez JM,
Griffiths E,
Harte R,
Hendrix DA,
Hunt T,
Jungreis I,
Kay M,
Khurana E,
Leng J,
Lin MF,
Loveland J,
Lu Z,
Manthravadi D,
Mariotti M,
Mudge J,
Mukherjee G,
Notredame C,
Pei BK,
Rodriguez JM,
Saunders G,
Sboner A,
Searle S,
Sisu C,
Snow C,
Steward C,
Tapanari E,
Tress ML,
van Baren MJ,
Washietl S,
Wilming L,
Zadissa A,
Zhang ZD,
Brent M,
Haussler D,
Valencia A,
Addleman N,
Alexander RP,
Auerbach RK,
Bettinger K,
Bhardwaj N,
Boyle AP,
Cao AR,
Cayting P,
Charos A,
Cheng Y,
Eastman C,
Euskirchen G,
Fleming JD,
Grubert F,
Habegger L,
Hariharan M,
Harmanci A,
Iyengar S,
Jin VX,
Karczewski KJ,
Kasowski M,
Lacroute P,
Lam H,
Lamarre-Vincent N,
Lian J,
Lindahl-Allen M,
Min RQ,
Miotto B,
Monahan H,
Moqtaderi Z,
Mu XM,
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Ouyang ZQ,
Patacsil D,
Raha D,
Ramirez L,
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Shi MY,
Slifer T,
Witt H,
Wu LF,
Xu XQ,
Yan KK,
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Struhl K,
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Penalva LO,
Karmakar S,
Bhanvadia RR,
Choudhury A,
Domanus M,
Ma LJ,
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Centanin L,
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Gruhl F,
Heermann S,
Hoeckendorf B,
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Mueller C,
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Schertel L,
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Wittbrodt B,
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Balasundaram G,
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Diegel MJ,
Dunn D,
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Reynolds AP,
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Stergachis AB,
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MacCoss MJ,
Navas P,
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Huang HY,
Li JJ,
Noble WS,
Bilmes JA,
Buske OJ,
Sahu AD,
Kharchenko PV,
Park PJ,
Baker D,
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Min R,
Encode Project Conso

Nature
  489 (7414): 57-74; Sep 6 2012  
[Abstract]
[DOI] [Full Text]

Landscape of transcription in human cells
Djebali S,
Davis CA,
Merkel A,
Dobin A,
Lassmann T,
Mortazavi A,
Tanzer A,
Lagarde J,
Lin W,
Schlesinger F,
Xue C,
Marinov GK,
Khatun J,
Williams BA,
Zaleski C,
Rozowsky J,
Röder M,
Kokocinski F,
Abdelhamid RF,
Alioto T,
Antoshechkin I,
Baer MT,
Bar NS,
Batut P,
Bell K,
Bell I,
Chakrabortty S,
Chen X,
Chrast J,
Curado J,
Derrien T,
Drenkow J,
Dumais E,
Dumais J,
Duttagupta R,
Falconnet E,
Fastuca M,
Fejes-Toth K,
Ferreira P,
Foissac S,
Fullwood MJ,
Gao H,
Gonzalez D,
Gordon A,
Gunawardena H,
Howald C,
Jha S,
Johnson R,
Kapranov P,
King B,
Kingswood C,
Luo OJ,
Park E,
Persaud K,
Preall JB,
Ribeca P,
Risk B,
Robyr D,
Sammeth M,
Schaffer L,
See LH,
Shahab A,
Skancke J,
Suzuki AM,
Takahashi H,
Tilgner H,
Trout D,
Walters N,
Wang H,
Wrobel J,
Yu Y,
Ruan X,
Hayashizaki Y,
Harrow J,
Gerstein M,
Hubbard T,
Reymond A,
Antonarakis SE,
Hannon G,
Giddings MC,
Ruan Y,
Wold B,
Carninci P,
Guig R,
Gingeras TR

Nature
  489 (7414): 101-108; Sep 6 2012  
[Abstract]
[Full Text]

MicroRNA93 Regulates Proliferation and Differentiation of Normal and Malignant Breast Stem Cells
Liu S,
Patel SH,
Ginestier C,
Ibarra I,
Martin-Trevino R,
Bai S,
McDermott SP,
Shang L,
Ke J,
Ou SJ,
Heath A,
Zhang KJ,
Korkaya H,
Clouthier SG,
Charafe-Jauffret E,
Birnbaum D,
Hannon GJ,
Wicha MS

PLoS Genetics
  8 (6): e1002751; Jun 2012   Nlm
[Abstract]
[DOI] [Full Text]

GAGE: A critical evaluation of genome assemblies and assembly algorithms
Salzberg SL,
Phillippy AM,
Zimin A,
Puiu D,
Magoc T,
Koren S,
Treangen TJ,
Schatz MC,
Delcher AL,
Roberts M,
Marcais G,
Pop M,
Yorke JA

Genome Res
  22 (3): 557-67; Mar 2012   NLM
[Abstract]
[DOI] [Full Text]

Ndfip1 regulates nuclear Pten import in vivo to promote neuronal survival following cerebral ischemia
Howitt J,
Lackovic J,
Low LH,
Naguib A,
Macintyre A,
Goh CP,
Callaway JK,
Hammond V,
Thomas T,
Dixon M,
Putz U,
Silke J,
Bartlett P,
Yang BL,
Kumar S,
Trotman LC,
Tan SS

Journal of Cell Biology
  196 (1): 29-36; Jan 2012  
[Abstract]
[DOI] [Full Text]

A genome-scale shRNA resource for transgenic RNAi in Drosophila
Ni JQ,
Zhou R,
Czech B,
Liu LP,
Holderbaum L,
Yang-Zhou DH,
Shim HS,
Tao R,
Handler D,
Karpowicz P,
Binari R,
Booker M,
Brennecke J,
Perkins LA,
Hannon GJ,
Perrimon N

Nature Methods
  8 (5): 405-7; May 2011  
[Abstract]
[DOI]

Chronic cisplatin treatment promotes enhanced damage repair and tumor progression in a mouse model of lung cancer
Oliver TG,
Mercer KL,
Sayles LC,
Burke JR,
Mendus D,
Lovejoy KS,
Cheng MH,
Subramanian A,
Mu D,
Powers S,
Crowley D,
Bronson RT,
Whittaker CA,
Bhutkar A,
Lippard SJ,
Golub T,
Thomale J,
Jacks T,
Sweet-Cordero EA

Genes Development
  24 (8): 837-852; Apr 2010   PMCID: PMC2854397
[Abstract]
[DOI] [Full Text] [PDF]

Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis
Dalloul RA,
Long JA,
Zimin AV,
Aslam L,
Beal K,
Blomberg LA,
Bouffard P,
Burt DW,
Crasta O,
Crooijmans RP,
Cooper K,
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Dodgson JB,
Dong JJ,
Evans C,
Frederickson KM,
Flicek P,
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Groenen MA,
Harkins TT,
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Jiang A,
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Kim H,
Kim KW,
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Langenberger D,
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Pertea G,
Prickett D,
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Qioa D,
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Tafer H,
Tu Z,
van Tassell CP,
Vilella AJ,
Williams KP,
Yorke JA,
Zhang L,
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Zhang X,
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Reed KM

Plos Biology
  8 (9): 2010  
[Abstract]
[DOI] [Full Text]

The B73 Maize Genome: Complexity, Diversity, and Dynamics
Schnable PS,
Ware DH,
Fulton RS,
Stein JC,
Wei FS,
Pasternak S,
Liang CZ,
Zhang JW,
Fulton L,
Graves TA,
Minx P,
Reily AD,
Courtney L,
Kruchowski SS,
Tomlinson C,
Strong C,
Delehaunty K,
Fronick C,
Courtney B,
Rock SM,
Belter E,
Du FY,
Kim K,
Abbott RM,
Cotton M,
Levy A,
Marchetto P,
Ochoa K,
Jackson SM,
Gillam B,
Chen WZ,
Yan L,
Higginbotham J,
Cardenas M,
Waligorski J,
Applebaum E,
Phelps L,
Falcone J,
Kanchi K,
Thane T,
Scimone A,
Thane N,
Henke J,
Wang T,
Ruppert J,
Shah N,
Rotter K,
Hodges J,
Ingenthron E,
Cordes M,
Kohlberg S,
Sgro J,
Delgado B,
Mead K,
Chinwalla A,
Leonard S,
Crouse K,
Collura K,
Kudrna D,
Currie J,
He RF,
Angelova A,
Rajasekar S,
Mueller T,
Lomeli R,
Scara G,
Ko A,
Delaney K,
Wissotski M,
Lopez G,
Campos D,
Braidotti M,
Ashley E,
Golser W,
Kim H,
Lee S,
Lin JK,
Dujmic Z,
Kim W,
Talag J,
Zuccolo A,
Fan C,
Sebastian A,
Kramer MR,
Spiegel L,
Nascimento L,
Zutavern T,
Miller B,
Ambroise C,
Muller S,
Spooner W,
Narechania A,
Ren LY,
Wei S,
Kumari S,
Faga BP,
Levy MJ,
McMahan L,
Van Buren P,
Vaughn MW,
Ying K,
Yeh CT,
Emrich SJ,
Jia Y,
Kalyanaraman A,
Hsia AP,
Barbazuk WB,
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Brutnell TP,
Carpita NC,
Chaparro C,
Chia JM,
Deragon JM,
Estill JC,
Fu Y,
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Han YJ,
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Liu ZJ,
Nagel DH,
McCann MC,
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Myers AM,
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The Sv40 Enhancer Is Composed of Multiple Functional Elements That Can Compensate for One Another
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Cell
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Duplications within Mutated Sv-40 Enhancers That Restore Enhancer Function
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