-
1
-
-
70349859881
-
DNA damage, aging, and cancer
-
Hoeijmakers JH. DNA damage, aging, and cancer. N Engl J Med 2009; 361:1475-1485.
-
(2009)
N Engl J Med
, vol.361
, pp. 1475-1485
-
-
Hoeijmakers, J.H.1
-
2
-
-
45449083227
-
DNA double-strand breaks: a potential causative factor for mammalian aging?
-
Li H, Mitchell JR, Hasty P. DNA double-strand breaks: a potential causative factor for mammalian aging? Mech Ageing Dev 2008; 129:416-424.
-
(2008)
Mech Ageing Dev
, vol.129
, pp. 416-424
-
-
Li, H.1
Mitchell, J.R.2
Hasty, P.3
-
3
-
-
34548150187
-
The role of nuclear architecture in genomic instability and ageing
-
Oberdoerffer P, Sinclair DA. The role of nuclear architecture in genomic instability and ageing. Nat. Rev. Mol. Cell. Biol. 2007; 8:692-702.
-
(2007)
Nat. Rev. Mol. Cell. Biol.
, vol.8
, pp. 692-702
-
-
Oberdoerffer, P.1
Sinclair, D.A.2
-
4
-
-
84867907645
-
The great unravelling: chromatin as a modulator of the aging process
-
O'Sullivan RJ, Karlseder J. The great unravelling: chromatin as a modulator of the aging process. Trends Biochem Sci 2012; 37:466-476.
-
(2012)
Trends Biochem Sci
, vol.37
, pp. 466-476
-
-
O'Sullivan, R.J.1
Karlseder, J.2
-
5
-
-
84860879005
-
Human transposon tectonics
-
Burns KH, Boeke JD. Human transposon tectonics. Cell 2012; 149:740-752.
-
(2012)
Cell
, vol.149
, pp. 740-752
-
-
Burns, K.H.1
Boeke, J.D.2
-
6
-
-
84855281420
-
Repetitive elements may comprise over two-thirds of the human genome
-
de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet 2011; 7:e1002384.
-
(2011)
PLoS Genet
, vol.7
-
-
de Koning, A.P.1
Gu, W.2
Castoe, T.A.3
Batzer, M.A.4
Pollock, D.D.5
-
7
-
-
80051997952
-
Dynamic interactions between transposable elements and their hosts
-
Levin HL, Moran JV. Dynamic interactions between transposable elements and their hosts. Nat Rev Genet 2011; 12:615-627.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 615-627
-
-
Levin, H.L.1
Moran, J.V.2
-
10
-
-
67650142756
-
Dynamics of transposable elements: towards a community ecology of the genome
-
Venner S, Feschotte C, Biemont C. Dynamics of transposable elements: towards a community ecology of the genome. Trends Genet 2009; 25:317-323.
-
(2009)
Trends Genet
, vol.25
, pp. 317-323
-
-
Venner, S.1
Feschotte, C.2
Biemont, C.3
-
11
-
-
84874957633
-
How do mammalian transposons induce genetic variation? A conceptual framework: the age, structure, allele frequency, and genome context of transposable elements may define their wide-ranging biological impacts
-
Akagi K, Li J, Symer DE. How do mammalian transposons induce genetic variation? A conceptual framework: the age, structure, allele frequency, and genome context of transposable elements may define their wide-ranging biological impacts. Bioessays 2013; 35:397-407.
-
(2013)
Bioessays
, vol.35
, pp. 397-407
-
-
Akagi, K.1
Li, J.2
Symer, D.E.3
-
13
-
-
33645068168
-
The human LINE-1 retrotransposon creates DNA double-strand breaks
-
Gasior SL, Wakeman TP, Xu B, Deininger PL. The human LINE-1 retrotransposon creates DNA double-strand breaks. J Mol Biol 2006; 357:1383-1393.
-
(2006)
J Mol Biol
, vol.357
, pp. 1383-1393
-
-
Gasior, S.L.1
Wakeman, T.P.2
Xu, B.3
Deininger, P.L.4
-
15
-
-
84862507347
-
Active human retrotransposons: variation and disease
-
Hancks DC, Kazazian HH, Jr. Active human retrotransposons: variation and disease. Curr Opin Genet Dev 2012; 22:191-203.
-
(2012)
Curr Opin Genet Dev
, vol.22
, pp. 191-203
-
-
Hancks, D.C.1
Kazazian Jr., H.H.2
-
16
-
-
77953880842
-
LINE-1 retrotransposition activity in human genomes
-
Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, Eichler EE, Badge RM, Moran JV. LINE-1 retrotransposition activity in human genomes. Cell 2010; 141:1159-1170.
-
(2010)
Cell
, vol.141
, pp. 1159-1170
-
-
Beck, C.R.1
Collier, P.2
Macfarlane, C.3
Malig, M.4
Kidd, J.M.5
Eichler, E.E.6
Badge, R.M.7
Moran, J.V.8
-
17
-
-
69349096044
-
L1 retrotransposition in human neural progenitor cells
-
Coufal NG, Garcia-Perez JL, Peng GE, Yeo GW, Mu Y, Lovci MT, Morell M, O'Shea KS, Moran JV, Gage FH. L1 retrotransposition in human neural progenitor cells. Nature 2009; 460:1127-1131.
-
(2009)
Nature
, vol.460
, pp. 1127-1131
-
-
Coufal, N.G.1
Garcia-Perez, J.L.2
Peng, G.E.3
Yeo, G.W.4
Mu, Y.5
Lovci, M.T.6
Morell, M.7
O'Shea, K.S.8
Moran, J.V.9
Gage, F.H.10
-
19
-
-
81855178276
-
Somatic retrotransposition alters the genetic landscape of the human brain
-
Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M and others. Somatic retrotransposition alters the genetic landscape of the human brain. Nature 2011; 479:534-537.
-
(2011)
Nature
, vol.479
, pp. 534-537
-
-
Baillie, J.K.1
Barnett, M.W.2
Upton, K.R.3
Gerhardt, D.J.4
Richmond, T.A.5
De Sapio, F.6
Brennan, P.M.7
Rizzu, P.8
Smith, S.9
Fell, M.10
-
20
-
-
84868032982
-
Singleneuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain
-
Evrony GD, Cai X, Lee E, Hills LB, Elhosary PC, Lehmann HS, Parker JJ, Atabay KD, Gilmore EC, Poduri A and others. Singleneuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 2012; 151:483-496.
-
(2012)
Cell
, vol.151
, pp. 483-496
-
-
Evrony, G.D.1
Cai, X.2
Lee, E.3
Hills, L.B.4
Elhosary, P.C.5
Lehmann, H.S.6
Parker, J.J.7
Atabay, K.D.8
Gilmore, E.C.9
Poduri, A.10
-
21
-
-
84865285978
-
Landscape of somatic retrotransposition in human cancers
-
Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, 3rd, Lohr JG, Harris CC, Ding L, Wilson RK and others. Landscape of somatic retrotransposition in human cancers. Science 2012; 337:967-971.
-
(2012)
Science
, vol.337
, pp. 967-971
-
-
Lee, E.1
Iskow, R.2
Yang, L.3
Gokcumen, O.4
Haseley, P.5
Luquette III, L.J.6
Lohr, J.G.7
Harris, C.C.8
Ding, L.9
Wilson, R.K.10
-
22
-
-
84875999688
-
Long interspersed element-1 (LINE-1): passenger or driver in human neoplasms?
-
Rodic N, Burns KH. Long interspersed element-1 (LINE-1): passenger or driver in human neoplasms? PLoS Genet 2013; 9:e1003402.
-
(2013)
PLoS Genet
, vol.9
-
-
Rodic, N.1
Burns, K.H.2
-
23
-
-
84875698271
-
Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma
-
Shukla R, Upton KR, Munoz-Lopez M, Gerhardt DJ, Fisher ME, Nguyen T, Brennan PM, Baillie JK, Collino A, Ghisletti S and others. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 2013; 153:101-111.
-
(2013)
Cell
, vol.153
, pp. 101-111
-
-
Shukla, R.1
Upton, K.R.2
Munoz-Lopez, M.3
Gerhardt, D.J.4
Fisher, M.E.5
Nguyen, T.6
Brennan, P.M.7
Baillie, J.K.8
Collino, A.9
Ghisletti, S.10
-
24
-
-
84870482898
-
Extensive somatic L1 retrotransposition in colorectal tumors
-
Solyom S, Ewing AD, Rahrmann EP, Doucet T, Nelson HH, Burns MB, Harris RS, Sigmon DF, Casella A, Erlanger B and others. Extensive somatic L1 retrotransposition in colorectal tumors. Genome Res 2012; 22:2328-2338.
-
(2012)
Genome Res
, vol.22
, pp. 2328-2338
-
-
Solyom, S.1
Ewing, A.D.2
Rahrmann, E.P.3
Doucet, T.4
Nelson, H.H.5
Burns, M.B.6
Harris, R.S.7
Sigmon, D.F.8
Casella, A.9
Erlanger, B.10
-
25
-
-
84878954836
-
Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements
-
De Cecco M, Criscione SW, Peckham EJ, Hillenmeyer S, Hamm EA, Manivannan J, Peterson AL, Kreiling JA, Neretti N, Sedivy JM. Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements. Aging Cell 2013; 12:247-256.
-
(2013)
Aging Cell
, vol.12
, pp. 247-256
-
-
De Cecco, M.1
Criscione, S.W.2
Peckham, E.J.3
Hillenmeyer, S.4
Hamm, E.A.5
Manivannan, J.6
Peterson, A.L.7
Kreiling, J.A.8
Neretti, N.9
Sedivy, J.M.10
-
26
-
-
79952609648
-
Age-associated increase in heterochromatic marks in murine and primate tissues
-
Kreiling JA, Tamamori-Adachi M, Sexton AN, Jeyapalan JC, Munoz-Najar U, Peterson AL, Manivannan J, Rogers ES, Pchelintsev NA, Adams PD and others. Age-associated increase in heterochromatic marks in murine and primate tissues. Aging Cell 2011; 10:292-304.
-
(2011)
Aging Cell
, vol.10
, pp. 292-304
-
-
Kreiling, J.A.1
Tamamori-Adachi, M.2
Sexton, A.N.3
Jeyapalan, J.C.4
Munoz-Najar, U.5
Peterson, A.L.6
Manivannan, J.7
Rogers, E.S.8
Pchelintsev, N.A.9
Adams, P.D.10
-
29
-
-
55549096355
-
Murine endogenous retroviruses
-
Stocking C, Kozak CA. Murine endogenous retroviruses. Cell Mol Life Sci 2008; 65:3383-3398.
-
(2008)
Cell Mol Life Sci
, vol.65
, pp. 3383-3398
-
-
Stocking, C.1
Kozak, C.A.2
-
30
-
-
84860920123
-
Of mice and men: the benefits of caloric restriction, exercise, and mimetics
-
Mercken EM, Carboneau BA, Krzysik-Walker SM, de Cabo R. Of mice and men: the benefits of caloric restriction, exercise, and mimetics. Ageing Res Rev 2012; 11:390-398.
-
(2012)
Ageing Res Rev
, vol.11
, pp. 390-398
-
-
Mercken, E.M.1
Carboneau, B.A.2
Krzysik-Walker, S.M.3
de Cabo, R.4
-
31
-
-
67650439330
-
Caloric restriction delays disease onset and mortality in rhesus monkeys
-
Colman RJ, Anderson RM, Johnson SC, Kastman EK, Kosmatka KJ, Beasley TM, Allison DB, Cruzen C, Simmons HA, Kemnitz JW and others. Caloric restriction delays disease onset and mortality in rhesus monkeys. Science 2009; 325:201-204.
-
(2009)
Science
, vol.325
, pp. 201-204
-
-
Colman, R.J.1
Anderson, R.M.2
Johnson, S.C.3
Kastman, E.K.4
Kosmatka, K.J.5
Beasley, T.M.6
Allison, D.B.7
Cruzen, C.8
Simmons, H.A.9
Kemnitz, J.W.10
-
32
-
-
84866163081
-
Impact of caloric restriction on health and survival in rhesus monkeys from the NIA study
-
Mattison JA, Roth GS, Beasley TM, Tilmont EM, Handy AM, Herbert RL, Longo DL, Allison DB, Young JE, Bryant M and others. Impact of caloric restriction on health and survival in rhesus monkeys from the NIA study. Nature 2012; 489:318-321.
-
(2012)
Nature
, vol.489
, pp. 318-321
-
-
Mattison, J.A.1
Roth, G.S.2
Beasley, T.M.3
Tilmont, E.M.4
Handy, A.M.5
Herbert, R.L.6
Longo, D.L.7
Allison, D.B.8
Young, J.E.9
Bryant, M.10
-
33
-
-
77953081850
-
A LINE-1 component to human aging: do LINE elements exact a longevity cost for evolutionary advantage?
-
St Laurent G, 3rd, Hammell N, McCaffrey TA. A LINE-1 component to human aging: do LINE elements exact a longevity cost for evolutionary advantage? Mech Ageing Dev 2010; 131:299-305.
-
(2010)
Mech Ageing Dev
, vol.131
, pp. 299-305
-
-
St Laurent III, G.1
Hammell, N.2
McCaffrey, T.A.3
-
34
-
-
84879890507
-
Functional impact of the human mobilome
-
Babatz TD, Burns KH. Functional impact of the human mobilome. Curr Opin Genet Dev 2013; 23:264-270.
-
(2013)
Curr Opin Genet Dev
, vol.23
, pp. 264-270
-
-
Babatz, T.D.1
Burns, K.H.2
-
35
-
-
84882682843
-
Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape
-
Shah PP, Donahue G, Otte GL, Capell BC, Nelson DM, Cao K, Aggarwala V, Cruickshanks HA, Rai TS, McBryan T and others. Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape. Genes Dev 2013; 27:1787-1799.
-
(2013)
Genes Dev
, vol.27
, pp. 1787-1799
-
-
Shah, P.P.1
Donahue, G.2
Otte, G.L.3
Capell, B.C.4
Nelson, D.M.5
Cao, K.6
Aggarwala, V.7
Cruickshanks, H.A.8
Rai, T.S.9
McBryan, T.10
-
36
-
-
77957814604
-
Reduced histone biosynthesis and chromatin changes arising from a damage signal at telomeres
-
O'Sullivan RJ, Kubicek S, Schreiber SL, Karlseder J. Reduced histone biosynthesis and chromatin changes arising from a damage signal at telomeres. Nat Struct Mol Biol 2010; 17:1218-1225.
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 1218-1225
-
-
O'Sullivan, R.J.1
Kubicek, S.2
Schreiber, S.L.3
Karlseder, J.4
-
37
-
-
84880585547
-
Lysosome-mediated processing of chromatin in senescence
-
Ivanov A, Pawlikowski J, Manoharan I, van Tuyn J, Nelson DM, Rai TS, Shah PP, Hewitt G, Korolchuk VI, Passos JF and others. Lysosome-mediated processing of chromatin in senescence. J Cell Biol 2013; 202:129-143.
-
(2013)
J Cell Biol
, vol.202
, pp. 129-143
-
-
Ivanov, A.1
Pawlikowski, J.2
Manoharan, I.3
van Tuyn, J.4
Nelson, D.M.5
Rai, T.S.6
Shah, P.P.7
Hewitt, G.8
Korolchuk, V.I.9
Passos, J.F.10
-
38
-
-
84900969225
-
Ink4a/Arf expression is a biomarker of aging
-
Krishnamurthy J, Torrice C, Ramsey MR, Kovalev GI, Al-Regaiey K, Su L, Sharpless NE. Ink4a/Arf expression is a biomarker of aging. J Clin Invest 2004; 114:1299-1307.
-
(2004)
J Clin Invest
, vol.114
, pp. 1299-1307
-
-
Krishnamurthy, J.1
Torrice, C.2
Ramsey, M.R.3
Kovalev, G.I.4
Al-Regaiey, K.5
Su, L.6
Sharpless, N.E.7
-
40
-
-
66149167336
-
DNA damage response and cellular senescence in tissues of aging mice
-
Wang C, Jurk D, Maddick M, Nelson G, Martin-Ruiz C, von Zglinicki T. DNA damage response and cellular senescence in tissues of aging mice. Aging Cell 2009; 8:311-323.
-
(2009)
Aging Cell
, vol.8
, pp. 311-323
-
-
Wang, C.1
Jurk, D.2
Maddick, M.3
Nelson, G.4
Martin-Ruiz, C.5
von Zglinicki, T.6
-
41
-
-
84855496921
-
Retrotransposition is associated with genome instability during chronological aging
-
Maxwell PH, Burhans WC, Curcio MJ. Retrotransposition is associated with genome instability during chronological aging. Proc Natl Acad Sci U S A 2011; 108:20376-20381.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 20376-20381
-
-
Maxwell, P.H.1
Burhans, W.C.2
Curcio, M.J.3
-
42
-
-
84876924361
-
Activation of transposable elements during aging and neuronal decline in Drosophila
-
Li W, Prazak L, Chatterjee N, Gruninger S, Krug L, Theodorou D, Dubnau J. Activation of transposable elements during aging and neuronal decline in Drosophila. Nat Neurosci 2013; 16:529-531.
-
(2013)
Nat Neurosci
, vol.16
, pp. 529-531
-
-
Li, W.1
Prazak, L.2
Chatterjee, N.3
Gruninger, S.4
Krug, L.5
Theodorou, D.6
Dubnau, J.7
-
43
-
-
84869186918
-
Postmitotic neurons develop a p21-dependent senescence-like phenotype driven by a DNA damage response
-
Jurk D, Wang C, Miwa S, Maddick M, Korolchuk V, Tsolou A, Gonos ES, Thrasivoulou C, Saffrey MJ, Cameron K and others. Postmitotic neurons develop a p21-dependent senescence-like phenotype driven by a DNA damage response. Aging Cell 2012; 11:996-1004.
-
(2012)
Aging Cell
, vol.11
, pp. 996-1004
-
-
Jurk, D.1
Wang, C.2
Miwa, S.3
Maddick, M.4
Korolchuk, V.5
Tsolou, A.6
Gonos, E.S.7
Thrasivoulou, C.8
Saffrey, M.J.9
Cameron, K.10
-
44
-
-
40449139336
-
Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health
-
Belancio VP, Hedges DJ, Deininger P. Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health. Genome Res 2008; 18:343-358.
-
(2008)
Genome Res
, vol.18
, pp. 343-358
-
-
Belancio, V.P.1
Hedges, D.J.2
Deininger, P.3
-
46
-
-
0242329885
-
Human Alu element retrotransposition induced by genotoxic stress
-
Hagan CR, Sheffield RF, Rudin CM. Human Alu element retrotransposition induced by genotoxic stress. Nat. Genet. 2003; 35:219-220.
-
(2003)
Nat. Genet.
, vol.35
, pp. 219-220
-
-
Hagan, C.R.1
Sheffield, R.F.2
Rudin, C.M.3
-
47
-
-
19644391725
-
Structural and functional characterization of noncoding repetitive RNAs transcribed in stressed human cells
-
Valgardsdottir R, Chiodi I, Giordano M, Cobianchi F, Riva S, Biamonti G. Structural and functional characterization of noncoding repetitive RNAs transcribed in stressed human cells. Mol. Biol. Cell 2005; 16:2597-2604.
-
(2005)
Mol. Biol. Cell
, vol.16
, pp. 2597-2604
-
-
Valgardsdottir, R.1
Chiodi, I.2
Giordano, M.3
Cobianchi, F.4
Riva, S.5
Biamonti, G.6
-
48
-
-
84891513140
-
Death by transposition - the enemy within?
-
BioEssays in press
-
Sedivy JM, Kreiling JA, Neretti N, De Cecco M, Criscione SW, Hofmann JW, Zhao X, Ito T, Peterson AL. Death by transposition - the enemy within? BioEssays in press.
-
-
-
Sedivy, J.M.1
Kreiling, J.A.2
Neretti, N.3
De Cecco, M.4
Criscione, S.W.5
Hofmann, J.W.6
Zhao, X.7
Ito, T.8
Peterson, A.L.9
-
49
-
-
79955552036
-
Effect of reverse transcriptase inhibitors on LINE-1 and Ty1 reverse transcriptase activities and on LINE-1 retrotransposition
-
Dai L, Huang Q, Boeke JD. Effect of reverse transcriptase inhibitors on LINE-1 and Ty1 reverse transcriptase activities and on LINE-1 retrotransposition. BMC Biochem 2011; 12:18.
-
(2011)
BMC Biochem
, vol.12
, pp. 18
-
-
Dai, L.1
Huang, Q.2
Boeke, J.D.3
-
50
-
-
0025107556
-
A deletion of the human betaglobin locus activation region causes a major alteration in chromatin structure and replication across the entire beta-globin locus
-
Forrester WC, Epner E, Driscoll MC, Enver T, Brice M, Papayannopoulou T, Groudine M. A deletion of the human betaglobin locus activation region causes a major alteration in chromatin structure and replication across the entire beta-globin locus. Genes Dev 1990; 4:1637-1649.
-
(1990)
Genes Dev
, vol.4
, pp. 1637-1649
-
-
Forrester, W.C.1
Epner, E.2
Driscoll, M.C.3
Enver, T.4
Brice, M.5
Papayannopoulou, T.6
Groudine, M.7
-
52
-
-
33845792555
-
CellProfiler: image analysis software for identifying and quantifying cell phenotypes
-
Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J and others. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol 2006; 7:R100.
-
(2006)
Genome Biol
, vol.7
-
-
Carpenter, A.E.1
Jones, T.R.2
Lamprecht, M.R.3
Clarke, C.4
Kang, I.H.5
Friman, O.6
Guertin, D.A.7
Chang, J.H.8
Lindquist, R.A.9
Moffat, J.10
-
53
-
-
77957739239
-
Positive regulation of euchromatic gene expression by HP1
-
Piacentini L, Pimpinelli S. Positive regulation of euchromatic gene expression by HP1. Fly (Austin) 2010; 4:299-301.
-
(2010)
Fly (Austin)
, vol.4
, pp. 299-301
-
-
Piacentini, L.1
Pimpinelli, S.2
-
54
-
-
58149510531
-
CellProfiler Analyst: data exploration and analysis software for complex image-based screens
-
Jones TR, Kang IH, Wheeler DB, Lindquist RA, Papallo A, Sabatini DM, Golland P, Carpenter AE. CellProfiler Analyst: data exploration and analysis software for complex image-based screens. BMC Bioinformatics 2008; 9:482.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 482
-
-
Jones, T.R.1
Kang, I.H.2
Wheeler, D.B.3
Lindquist, R.A.4
Papallo, A.5
Sabatini, D.M.6
Golland, P.7
Carpenter, A.E.8
-
55
-
-
80855144457
-
Nuclear protein accumulation in cellular senescence and organismal aging revealed with a novel single-cell resolution fluorescence microscopy assay
-
De Cecco M, Jeyapalan J, Zhao X, Tamamori-Adachi M, Sedivy JM. Nuclear protein accumulation in cellular senescence and organismal aging revealed with a novel single-cell resolution fluorescence microscopy assay. Aging (Albany NY) 2011; 3:955-967.
-
(2011)
Aging (Albany NY)
, vol.3
, pp. 955-967
-
-
De Cecco, M.1
Jeyapalan, J.2
Zhao, X.3
Tamamori-Adachi, M.4
Sedivy, J.M.5
-
56
-
-
40349098062
-
macroH2A1-dependent silencing of endogenous murine leukemia viruses
-
Changolkar LN, Singh G, Pehrson JR. macroH2A1-dependent silencing of endogenous murine leukemia viruses. Mol. Cell. Biol. 2008; 28:2059-2065.
-
(2008)
Mol. Cell. Biol.
, vol.28
, pp. 2059-2065
-
-
Changolkar, L.N.1
Singh, G.2
Pehrson, J.R.3
-
57
-
-
79960058683
-
Amplification-free library preparation for paired-end Illumina sequencing
-
Kozarewa I, Turner DJ. Amplification-free library preparation for paired-end Illumina sequencing. Methods Mol. Biol. 2011; 733:257-266.
-
(2011)
Methods Mol. Biol.
, vol.733
, pp. 257-266
-
-
Kozarewa, I.1
Turner, D.J.2
-
58
-
-
57049122389
-
A large genome center's improvements to the Illumina sequencing system
-
Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ. A large genome center's improvements to the Illumina sequencing system. Nat. Methods 2008; 5:1005-1010.
-
(2008)
Nat. Methods
, vol.5
, pp. 1005-1010
-
-
Quail, M.A.1
Kozarewa, I.2
Smith, F.3
Scally, A.4
Stephens, P.J.5
Durbin, R.6
Swerdlow, H.7
Turner, D.J.8
-
59
-
-
75949108066
-
Galaxy: a web-based genome analysis tool for experimentalists
-
Chapter 19:Unit 19 10 1-21
-
Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. 2010; Chapter 19:Unit 19 10 1-21.
-
(2010)
Curr. Protoc. Mol. Biol.
-
-
Blankenberg, D.1
Von Kuster, G.2
Coraor, N.3
Ananda, G.4
Lazarus, R.5
Mangan, M.6
Nekrutenko, A.7
Taylor, J.8
-
60
-
-
25844449770
-
Galaxy: a platform for interactive large-scale genome analysis
-
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J and others. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005; 15:1451-1455.
-
(2005)
Genome Res
, vol.15
, pp. 1451-1455
-
-
Giardine, B.1
Riemer, C.2
Hardison, R.C.3
Burhans, R.4
Elnitski, L.5
Shah, P.6
Zhang, Y.7
Blankenberg, D.8
Albert, I.9
Taylor, J.10
-
61
-
-
77955801615
-
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010; 11:R86.
-
(2010)
Genome Biol
, vol.11
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
62
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25:1105-1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
63
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010; 28:511-515.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
64
-
-
77953935308
-
Estimating enrichment of repetitive elements from high-throughput sequence data
-
Day DS, Luquette LJ, Park PJ, Kharchenko PV. Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biol. 2010; 11:R69.
-
(2010)
Genome Biol
, vol.11
-
-
Day, D.S.1
Luquette, L.J.2
Park, P.J.3
Kharchenko, P.V.4
-
65
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10:R25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
66
-
-
50649089207
-
RNAseq: an assessment of technical reproducibility and comparison with gene expression arrays
-
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNAseq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008; 18:1509-1517.
-
(2008)
Genome Res
, vol.18
, pp. 1509-1517
-
-
Marioni, J.C.1
Mason, C.E.2
Mane, S.M.3
Stephens, M.4
Gilad, Y.5
-
67
-
-
75249087100
-
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010; 26:139-140.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
68
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W. Differential expression analysis for sequence count data. Genome. Biol. 2010; 11:R106.
-
(2010)
Genome. Biol.
, vol.11
-
-
Anders, S.1
Huber, W.2
-
69
-
-
0042424602
-
Statistical significance for genomewide studies
-
Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 2003; 100:9440-9445.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
|