-
1
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
-
Mikkelsen, T.S.; Ku, M.; Jaffe, D.B.; Issac, B.; Lieberman, E.; Giannoukos, G.; Alvarez, P.; Brockman, W.; Kim, T.K.; Koche, R.P.; et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448, 553-560.
-
(2007)
Nature
, vol.448
, pp. 553-560
-
-
Mikkelsen, T.S.1
Ku, M.2
Jaffe, D.B.3
Issac, B.4
Lieberman, E.5
Giannoukos, G.6
Alvarez, P.7
Brockman, W.8
Kim, T.K.9
Koche, R.P.10
-
2
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
Robertson, G.; Hirst, M.; Bainbridge, M.; Bilenky, M.; Zhao, Y.; Zeng, T.; Euskirchen, G.; Bernier, B.; Varhol, R.; Delaney, A.; et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 2007, 4, 651-657.
-
(2007)
Nat. Methods.
, vol.4
, pp. 651-657
-
-
Robertson, G.1
Hirst, M.2
Bainbridge, M.3
Bilenky, M.4
Zhao, Y.5
Zeng, T.6
Euskirchen, G.7
Bernier, B.8
Varhol, R.9
Delaney, A.10
-
3
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
Barski, A.; Cuddapah, S.; Cui, K.; Roh, T.Y.; Schones, D.E.; Wang, Z.; Wei, G.; Chepelev, I.; Zhao, K. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129, 823-837.
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.Y.4
Schones, D.E.5
Wang, Z.6
Wei, G.7
Chepelev, I.8
Zhao, K.9
-
4
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson, D.S.; Mortazavi, A.; Myers, R.M.; Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007, 316, 1497-1502.
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
5
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi, A.; Williams, B.A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5, 621-628.
-
(2008)
Nat. Methods.
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
6
-
-
50649089207
-
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
-
Marioni, J.C.; Mason, C.E.; Mane, S.M.; Stephens, M.; Gilad, Y. RNA-seq: 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
-
7
-
-
77952734605
-
Conservation and divergence of methylation patterning in plants and animals
-
Feng, S.; Cokus, S.J.; Zhang, X.; Chen, P.Y.; Bostick, M.; Goll, M.G.; Hetzel, J.; Jain, J.; Strauss, S.H.; Halpern, M.E.; et al. Conservation and divergence of methylation patterning in plants and animals. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 8689-8694.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 8689-8694
-
-
Feng, S.1
Cokus, S.J.2
Zhang, X.3
Chen, P.Y.4
Bostick, M.5
Goll, M.G.6
Hetzel, J.7
Jain, J.8
Strauss, S.H.9
Halpern, M.E.10
-
8
-
-
65549107163
-
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
-
Brunner, A.L.; Johnson, D.S.; Kim, S.W.; Valouev, A.; Reddy, T.E.; Neff, N.F.; Anton, E.; Medina, C.; Nguyen, L.; Chiao, E.; et al. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 2009, 19, 1044-1056.
-
(2009)
Genome Res
, vol.19
, pp. 1044-1056
-
-
Brunner, A.L.1
Johnson, D.S.2
Kim, S.W.3
Valouev, A.4
Reddy, T.E.5
Neff, N.F.6
Anton, E.7
Medina, C.8
Nguyen, L.9
Chiao, E.10
-
9
-
-
77449153454
-
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
-
Gu, H.; Bock, C.; Mikkelsen, T.S.; Jager, N.; Smith, Z.D.; Tomazou, E.; Gnirke, A.; Lander, E.S.; Meissner, A. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat. Methods 2010, 7, 133-136.
-
(2010)
Nat. Methods.
, vol.7
, pp. 133-136
-
-
Gu, H.1
Bock, C.2
Mikkelsen, T.S.3
Jager, N.4
Smith, Z.D.5
Tomazou, E.6
Gnirke, A.7
Lander, E.S.8
Meissner, A.9
-
10
-
-
49649125042
-
Genome-scale DNA methylation maps of pluripotent and differentiated cells
-
Meissner, A.; Mikkelsen, T.S.; Gu, H.; Wernig, M.; Hanna, J.; Sivachenko, A.; Zhang, X.; Bernstein, B.E.; Nusbaum, C.; Jaffe, D.B.; et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008, 454, 766-770.
-
(2008)
Nature
, vol.454
, pp. 766-770
-
-
Meissner, A.1
Mikkelsen, T.S.2
Gu, H.3
Wernig, M.4
Hanna, J.5
Sivachenko, A.6
Zhang, X.7
Bernstein, B.E.8
Nusbaum, C.9
Jaffe, D.B.10
-
11
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin, J.; Li, R.; Raes, J.; Arumugam, M.; Burgdorf, K.S.; Manichanh, C.; Nielsen, T.; Pons, N.; Levenez, F.; Yamada, T.; et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464, 59-65.
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
Li, R.2
Raes, J.3
Arumugam, M.4
Burgdorf, K.S.5
Manichanh, C.6
Nielsen, T.7
Pons, N.8
Levenez, F.9
Yamada, T.10
-
12
-
-
55549089660
-
Accurate whole human genome sequencing using reversible terminator chemistry
-
Bentley, D.R.; Balasubramanian, S.; Swerdlow, H.P.; Smith, G.P.; Milton, J.; Brown, C.G.; Hall, K.P.; Evers, D.J.; Barnes, C.L.; Bignell, H.R.; et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456, 53-59.
-
(2008)
Nature
, vol.456
, pp. 53-59
-
-
Bentley, D.R.1
Balasubramanian, S.2
Swerdlow, H.P.3
Smith, G.P.4
Milton, J.5
Brown, C.G.6
Hall, K.P.7
Evers, D.J.8
Barnes, C.L.9
Bignell, H.R.10
-
13
-
-
55549097849
-
The diploid genome sequence of an Asian individual
-
Wang, J.; Wang, W.; Li, R.; Li, Y.; Tian, G.; Goodman, L.; Fan, W.; Zhang, J.; Li, J.; Zhang, J.; et al. The diploid genome sequence of an Asian individual. Nature 2008, 456, 60-65.
-
(2008)
Nature
, vol.456
, pp. 60-65
-
-
Wang, J.1
Wang, W.2
Li, R.3
Li, Y.4
Tian, G.5
Goodman, L.6
Fan, W.7
Zhang, J.8
Li, J.9
Zhang, J.10
-
14
-
-
69249232047
-
A highly annotated whole-genome sequence of a Korean individual
-
Kim, J.I.; Ju, Y.S.; Park, H.; Kim, S.; Lee, S.; Yi, J.H.; Mudge, J.; Miller, N.A.; Hong, D.; Bell, C.J.; et al. A highly annotated whole-genome sequence of a Korean individual. Nature 2009, 460, 1011-1015.
-
(2009)
Nature
, vol.460
, pp. 1011-1015
-
-
Kim, J.I.1
Ju, Y.S.2
Park, H.3
Kim, S.4
Lee, S.5
Yi, J.H.6
Mudge, J.7
Miller, N.A.8
Hong, D.9
Bell, C.J.10
-
15
-
-
55549101623
-
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome
-
Ley, T.J.; Mardis, E.R.; Ding, L.; Fulton, B.; McLellan, M.D.; Chen, K.; Dooling, D.; Dunford-Shore, B.H.; McGrath, S.; Hickenbotham, M.; et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 2008, 456, 66-72.
-
(2008)
Nature
, vol.456
, pp. 66-72
-
-
Ley, T.J.1
Mardis, E.R.2
Ding, L.3
Fulton, B.4
McLellan, M.D.5
Chen, K.6
Dooling, D.7
Dunford-Shore, B.H.8
McGrath, S.9
Hickenbotham, M.10
-
16
-
-
77950458649
-
Transcriptome genetics using second generation sequencing in a Caucasian population
-
Montgomery, S.B.; Sammeth, M.; Gutierrez-Arcelus, M.; Lach, R.P.; Ingle, C.; Nisbett, J.; Guigo, R.; Dermitzakis, E.T. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 2010, 464, 773-777.
-
(2010)
Nature
, vol.464
, pp. 773-777
-
-
Montgomery, S.B.1
Sammeth, M.2
Gutierrez-Arcelus, M.3
Lach, R.P.4
Ingle, C.5
Nisbett, J.6
Guigo, R.7
Dermitzakis, E.T.8
-
17
-
-
77950460661
-
Understanding mechanisms underlying human gene expression variation with RNA sequencing
-
Pickrell, J.K.; Marioni, J.C.; Pai, A.A.; Degner, J.F.; Engelhardt, B.E.; Nkadori, E.; Veyrieras, J.B.; Stephens, M.; Gilad, Y.; Pritchard, J.K. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 2010, 464, 768-772.
-
(2010)
Nature
, vol.464
, pp. 768-772
-
-
Pickrell, J.K.1
Marioni, J.C.2
Pai, A.A.3
Degner, J.F.4
Engelhardt, B.E.5
Nkadori, E.6
Veyrieras, J.B.7
Stephens, M.8
Gilad, Y.9
Pritchard, J.K.10
-
18
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
Nagalakshmi, U.; Wang, Z.; Waern, K.; Shou, C.; Raha, D.; Gerstein, M.; Snyder, M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320, 1344-1349.
-
(2008)
Science
, vol.320
, pp. 1344-1349
-
-
Nagalakshmi, U.1
Wang, Z.2
Waern, K.3
Shou, C.4
Raha, D.5
Gerstein, M.6
Snyder, M.7
-
19
-
-
70349668297
-
Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing
-
Qi, W.; Kaser, M.; Roltgen, K.; Yeboah-Manu, D.; Pluschke, G. Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing. PLoS Pathog. 2009, 5, e1000580.
-
(2009)
PLoS Pathog
, vol.5
-
-
Qi, W.1
Kaser, M.2
Roltgen, K.3
Yeboah-Manu, D.4
Pluschke, G.5
-
20
-
-
70349577932
-
A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528
-
Studholme, D.J.; Ibanez, S.G.; MacLean, D.; Dangl, J.L.; Chang, J.H.; Rathjen, J.P. A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528. BMC Genomics 2009, 10, 395.
-
(2009)
BMC Genomics
, vol.10
, pp. 395
-
-
Studholme, D.J.1
Ibanez, S.G.2
Maclean, D.3
Dangl, J.L.4
Chang, J.H.5
Rathjen, J.P.6
-
21
-
-
77950400446
-
Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear
-
Lindqvist, C.; Schuster, S.C.; Sun, Y.; Talbot, S.L.; Qi, J.; Ratan, A.; Tomsho, L.P.; Kasson, L.; Zeyl, E.; Aars, J.; et al. Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 5053-5057.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 5053-5057
-
-
Lindqvist, C.1
Schuster, S.C.2
Sun, Y.3
Talbot, S.L.4
Qi, J.5
Ratan, A.6
Tomsho, L.P.7
Kasson, L.8
Zeyl, E.9
Aars, J.10
-
22
-
-
56749119854
-
Sequencing the nuclear genome of the extinct woolly mammoth
-
Miller, W.; Drautz, D.I.; Ratan, A.; Pusey, B.; Qi, J.; Lesk, A.M.; Tomsho, L.P.; Packard, M.D.; Zhao, F.; Sher, A.; et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 2008, 456, 387-390.
-
(2008)
Nature
, vol.456
, pp. 387-390
-
-
Miller, W.1
Drautz, D.I.2
Ratan, A.3
Pusey, B.4
Qi, J.5
Lesk, A.M.6
Tomsho, L.P.7
Packard, M.D.8
Zhao, F.9
Sher, A.10
-
23
-
-
39649117755
-
The impact of next-generation sequencing technology on genetics
-
Mardis, E.R. The impact of next-generation sequencing technology on genetics. Trends. Genet. 2008, 24, 133-141.
-
(2008)
Trends. Genet.
, vol.24
, pp. 133-141
-
-
Mardis, E.R.1
-
24
-
-
72849144434
-
Sequencing technologies - the next generation
-
Metzker, M.L. Sequencing technologies - the next generation. Nat. Rev. Genet. 2010, 11, 31-46.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 31-46
-
-
Metzker, M.L.1
-
25
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies, M.; Egholm, M.; Altman, W.E.; Attiya, S.; Bader, J.S.; Bemben, L.A.; Berka, J.; Braverman, M.S.; Chen, Y.J.; Chen, Z.; et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437, 376-380.
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
Berka, J.7
Braverman, M.S.8
Chen, Y.J.9
Chen, Z.10
-
27
-
-
41749104588
-
Single-molecule DNA sequencing of a viral genome
-
Harris, T.D.; Buzby, P.R.; Babcock, H.; Beer, E.; Bowers, J.; Braslavsky, I.; Causey, M.; Colonell, J.; Dimeo, J.; Efcavitch, J.W.; et al. Single-molecule DNA sequencing of a viral genome. Science 2008, 320, 106-109.
-
(2008)
Science
, vol.320
, pp. 106-109
-
-
Harris, T.D.1
Buzby, P.R.2
Babcock, H.3
Beer, E.4
Bowers, J.5
Braslavsky, I.6
Causey, M.7
Colonell, J.8
Dimeo, J.9
Efcavitch, J.W.10
-
28
-
-
58149234737
-
Real-time DNA sequencing from single polymerase molecules
-
Eid, J.; Fehr, A.; Gray, J.; Luong, K.; Lyle, J.; Otto, G.; Peluso, P.; Rank, D.; Baybayan, P.; Bettman, B.; et al. Real-time DNA sequencing from single polymerase molecules. Science 2009, 323, 133-138.
-
(2009)
Science
, vol.323
, pp. 133-138
-
-
Eid, J.1
Fehr, A.2
Gray, J.3
Luong, K.4
Lyle, J.5
Otto, G.6
Peluso, P.7
Rank, D.8
Baybayan, P.9
Bettman, B.10
-
29
-
-
70449701942
-
Sense from sequence reads: Methods for alignment and assembly
-
Flicek, P.; Birney, E. Sense from sequence reads: methods for alignment and assembly. Nat. Methods 2009, 6, S6-S12.
-
(2009)
Nat. Methods.
, vol.6
-
-
Flicek, P.1
Birney, E.2
-
30
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith, T.F.; Waterman, M.S. Identification of common molecular subsequences. J. Mol. Biol. 1981, 147, 195-197.
-
(1981)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
31
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li, H.; Ruan, J.; Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008, 18, 1851-1858.
-
(2008)
Genome Res
, vol.18
, pp. 1851-1858
-
-
Li, H.1
Ruan, J.2
Durbin, R.3
-
32
-
-
40049104732
-
SOAP: Short oligonucleotide alignment program
-
Li, R.; Li, Y.; Kristiansen, K.; Wang, J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24, 713-714.
-
(2008)
Bioinformatics
, vol.24
, pp. 713-714
-
-
Li, R.1
Li, Y.2
Kristiansen, K.3
Wang, J.4
-
33
-
-
54949110994
-
ZOOM! Zillions of oligos mapped
-
Lin, H.; Zhang, Z.; Zhang, M.Q.; Ma, B.; Li, M. ZOOM! Zillions of oligos mapped. Bioinformatics 2008, 24, 2431-2437.
-
(2008)
Bioinformatics
, vol.24
, pp. 2431-2437
-
-
Lin, H.1
Zhang, Z.2
Zhang, M.Q.3
Ma, B.4
Li, M.5
-
34
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B.; Trapnell, C.; Pop, M.; Salzberg, S.L. 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
-
35
-
-
53749083993
-
SeqMap: Mapping massive amount of oligonucleotides to the genome
-
Jiang, H.; Wong, W.H. SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 2008, 24, 2395-2396.
-
(2008)
Bioinformatics
, vol.24
, pp. 2395-2396
-
-
Jiang, H.1
Wong, W.H.2
-
36
-
-
18744383071
-
GMAP: A genomic mapping and alignment program for mRNA and EST sequences
-
Wu, T.D.; Watanabe, C.K. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005, 21, 1859-1875.
-
(2005)
Bioinformatics
, vol.21
, pp. 1859-1875
-
-
Wu, T.D.1
Watanabe, C.K.2
-
37
-
-
70450177746
-
BFAST: An alignment tool for large scale genome resequencing
-
Homer, N.; Merriman, B.; Nelson, S.F. BFAST: an alignment tool for large scale genome resequencing. PLoS ONE 2009, 4, e7767.
-
(2009)
PLoS ONE
, vol.4
-
-
Homer, N.1
Merriman, B.2
Nelson, S.F.3
-
38
-
-
63549114801
-
PASS: A program to align short sequences
-
Campagna, D.; Albiero, A.; Bilardi, A.; Caniato, E.; Forcato, C.; Manavski, S.; Vitulo, N.; Valle, G. PASS: a program to align short sequences. Bioinformatics 2009, 25, 967-968.
-
(2009)
Bioinformatics
, vol.25
, pp. 967-968
-
-
Campagna, D.1
Albiero, A.2
Bilardi, A.3
Caniato, E.4
Forcato, C.5
Manavski, S.6
Vitulo, N.7
Valle, G.8
-
39
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H.; Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25, 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
40
-
-
67049159825
-
SHRiMP: Accurate mapping of short color-space reads
-
Rumble, S.M.; Lacroute, P.; Dalca, A.V.; Fiume, M.; Sidow, A.; Brudno, M. SHRiMP: accurate mapping of short color-space reads. PLoS Comput. Biol. 2009, 5, e1000386.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Rumble, S.M.1
Lacroute, P.2
Dalca, A.V.3
Fiume, M.4
Sidow, A.5
Brudno, M.6
-
41
-
-
77957272611
-
A survey of sequence alignment algorithms for next-generation sequencing
-
Li, H.; Homer, N. A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinform. 2010.11, 473-483.
-
(2010)
Brief. Bioinform.
, vol.11
, pp. 473-483
-
-
Li, H.1
Homer, N.2
-
42
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren, B.; Robert, F.; Wyrick, J.J.; Aparicio, O.; Jennings, E.G.; Simon, I.; Zeitlinger, J.; Schreiber, J.; Hannett, N.; Kanin, E.; et al. Genome-wide location and function of DNA binding proteins. Science 2000, 290, 2306-2309.
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
Aparicio, O.4
Jennings, E.G.5
Simon, I.6
Zeitlinger, J.7
Schreiber, J.8
Hannett, N.9
Kanin, E.10
-
43
-
-
0035945567
-
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
-
Iyer, V.R.; Horak, C.E.; Scafe, C.S.; Botstein, D.; Snyder, M.; Brown, P.O. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 2001, 409, 533-538.
-
(2001)
Nature
, vol.409
, pp. 533-538
-
-
Iyer, V.R.1
Horak, C.E.2
Scafe, C.S.3
Botstein, D.4
Snyder, M.5
Brown, P.O.6
-
44
-
-
0034934774
-
Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
-
Lieb, J.D.; Liu, X.; Botstein, D.; Brown, P.O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 2001, 28, 327-334.
-
(2001)
Nat. Genet.
, vol.28
, pp. 327-334
-
-
Lieb, J.D.1
Liu, X.2
Botstein, D.3
Brown, P.O.4
-
45
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee, T.I.; Rinaldi, N.J.; Robert, F.; Odom, D.T.; Bar-Joseph, Z.; Gerber, G.K.; Hannett, N.M.; Harbison, C.T.; Thompson, C.M.; Simon, I.; et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298, 799-804.
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
-
46
-
-
77954041808
-
HPeak: An HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
-
Qin, Z.S.; Yu, J.; Shen, J.; Maher, C.A.; Hu, M.; Kalyana-Sundaram, S.; Yu, J.; Chinnaiyan, A.M. HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics 2010, 11, 369.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 369
-
-
Qin, Z.S.1
Yu, J.2
Shen, J.3
Maher, C.A.4
Hu, M.5
Kalyana-Sundaram, S.6
Yu, J.7
Chinnaiyan, A.M.8
-
47
-
-
77949916244
-
On the detection and refinement of transcription factor binding sites using ChIP-Seq data
-
Hu, M.; Yu, J.; Taylor, J.M.; Chinnaiyan, A.M.; Qin, Z.S. On the detection and refinement of transcription factor binding sites using ChIP-Seq data. Nucleic Acids Res. 2010, 38, 2154-2167.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 2154-2167
-
-
Hu, M.1
Yu, J.2
Taylor, J.M.3
Chinnaiyan, A.M.4
Qin, Z.S.5
-
48
-
-
77952103123
-
An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression
-
Yu, J.; Yu, J.; Mani, R.S.; Cao, Q.; Brenner, C.J.; Cao, X.; Wang, X.; Wu, L.; Li, J.; Hu, M.; et al. An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression. Cancer Cell 2010, 17, 443-454.
-
(2010)
Cancer Cell
, vol.17
, pp. 443-454
-
-
Yu, J.1
Yu, J.2
Mani, R.S.3
Cao, Q.4
Brenner, C.J.5
Cao, X.6
Wang, X.7
Wu, L.8
Li, J.9
Hu, M.10
-
49
-
-
54949147307
-
F-Seq: A feature density estimator for high-throughput sequence tags
-
Boyle, A.P.; Guinney, J.; Crawford, G.E.; Furey, T.S. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 2008, 24, 2537-2538.
-
(2008)
Bioinformatics
, vol.24
, pp. 2537-2538
-
-
Boyle, A.P.1
Guinney, J.2
Crawford, G.E.3
Furey, T.S.4
-
50
-
-
60849117520
-
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
-
Nix, D.A.; Courdy, S.J.; Boucher, K.M. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics 2008, 9, 523.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 523
-
-
Nix, D.A.1
Courdy, S.J.2
Boucher, K.M.3
-
51
-
-
70449434105
-
BayesPeak: Bayesian analysis of ChIP-seq data
-
Spyrou, C.; Stark, R.; Lynch, A.G.; Tavare, S. BayesPeak: Bayesian analysis of ChIP-seq data. BMC Bioinformatics 2009, 10, 299.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 299
-
-
Spyrou, C.1
Stark, R.2
Lynch, A.G.3
Tavare, S.4
-
52
-
-
60149112271
-
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
-
Rozowsky, J.; Euskirchen, G.; Auerbach, R.K.; Zhang, Z.D.; Gibson, T.; Bjornson, R.; Carriero, N.; Snyder, M.; Gerstein, M.B. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat. Biotechnol. 2009, 27, 66-75.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 66-75
-
-
Rozowsky, J.1
Euskirchen, G.2
Auerbach, R.K.3
Zhang, Z.D.4
Gibson, T.5
Bjornson, R.6
Carriero, N.7
Snyder, M.8
Gerstein, M.B.9
-
53
-
-
57449100870
-
Design and analysis of ChIP-seq experiments for DNA-binding proteins
-
Kharchenko, P.V.; Tolstorukov, M.Y.; Park, P.J. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotechnol. 2008, 26, 1351-1359.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1351-1359
-
-
Kharchenko, P.V.1
Tolstorukov, M.Y.2
Park, P.J.3
-
54
-
-
52649132425
-
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
-
Jothi, R.; Cuddapah, S.; Barski, A.; Cui, K.; Zhao, K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res. 2008, 36, 5221-5231.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 5221-5231
-
-
Jothi, R.1
Cuddapah, S.2
Barski, A.3
Cui, K.4
Zhao, K.5
-
55
-
-
50849090969
-
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
-
Valouev, A.; Johnson, D.S.; Sundquist, A.; Medina, C.; Anton, E.; Batzoglou, S.; Myers, R.M.; Sidow, A. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods 2008, 5, 829-834.
-
(2008)
Nat. Methods.
, vol.5
, pp. 829-834
-
-
Valouev, A.1
Johnson, D.S.2
Sundquist, A.3
Medina, C.4
Anton, E.5
Batzoglou, S.6
Myers, R.M.7
Sidow, A.8
-
56
-
-
53849146020
-
Model-based Analysis of ChIP-Seq (MACS)
-
Zhang, Y.; Liu, T.; Meyer, C.A.; Eeckhoute, J.; Johnson, D.S.; Bernstein, B.E.; Nussbaum, C.; Myers, R.M.; Brown, M.; Li, W.; Liu, X.S. Model-based Analysis of ChIP-Seq (MACS). Genome Biol. 2008, 9, R137.
-
(2008)
Genome Biol
, vol.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nussbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
Liu, X.S.11
-
57
-
-
48249140621
-
FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology
-
Fejes, A.P.; Robertson, G.; Bilenky, M.; Varhol, R.; Bainbridge, M.; Jones, S.J. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 2008, 24, 1729-1730.
-
(2008)
Bioinformatics
, vol.24
, pp. 1729-1730
-
-
Fejes, A.P.1
Robertson, G.2
Bilenky, M.3
Varhol, R.4
Bainbridge, M.5
Jones, S.J.6
-
58
-
-
79952090817
-
PICS: Probabilistic Inference for ChIP-seq
-
in press
-
Zhang, X.; Robertson, G.; Krzywinski, M.; Ning, K.; Droit, A.; Jones, S.; Gottardo, R. PICS: Probabilistic Inference for ChIP-seq. Biometrics 2010, in press.
-
(2010)
Biometrics
-
-
Zhang, X.1
Robertson, G.2
Krzywinski, M.3
Ning, K.4
Droit, A.5
Jones, S.6
Gottardo, R.7
-
59
-
-
74549114755
-
A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
-
Laajala, T.D.; Raghav, S.; Tuomela, S.; Lahesmaa, R.; Aittokallio, T.; Elo, L.L. A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics 2009, 10, 618.
-
(2009)
BMC Genomics
, vol.10
, pp. 618
-
-
Laajala, T.D.1
Raghav, S.2
Tuomela, S.3
Lahesmaa, R.4
Aittokallio, T.5
Elo, L.L.6
-
60
-
-
77955368935
-
Evaluation of algorithm performance in ChIP-seq peak detection
-
Wilbanks, E.G.; Facciotti, M.T. Evaluation of algorithm performance in ChIP-seq peak detection. PLoS ONE 2010, 5, e11471.
-
(2010)
PLoS ONE
, vol.5
-
-
Wilbanks, E.G.1
Facciotti, M.T.2
-
61
-
-
0001677717
-
Controlling the false discovery rate: A pratical and powerful approach to multiple testing
-
Benjamini, Y.; Hochberg, Y. Controlling the false discovery rate: a pratical and powerful approach to multiple testing. J. Royal Stat. Soc. B 1995, 57, 289-300.
-
(1995)
J. Royal Stat. Soc. B.
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
62
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher, V.G.; Tibshirani, R.; Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 5116-5121.
-
(2001)
Proc. Natl. Acad. Sci. U. S. A.
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
64
-
-
55749094855
-
An integrated software system for analyzing ChIP-chip and ChIP-seq data
-
Ji, H.; Jiang, H.; Ma, W.; Johnson, D.S.; Myers, R.M.; Wong, W.H. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol. 2008, 26, 1293-1300.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1293-1300
-
-
Ji, H.1
Jiang, H.2
Ma, W.3
Johnson, D.S.4
Myers, R.M.5
Wong, W.H.6
-
65
-
-
0000342467
-
Statistical Inference for Probabilistic Functions of Finite State Markov Chains
-
Baum, L.E.; Petrie, T. Statistical Inference for Probabilistic Functions of Finite State Markov Chains. Ann. Math. Stat. 1966, 37, 1554-1563.
-
(1966)
Ann. Math. Stat.
, vol.37
, pp. 1554-1563
-
-
Baum, L.E.1
Petrie, T.2
-
66
-
-
0034047548
-
Bayesian segmentation of protein secondary structure
-
Schmidler, S.C.; Liu, J.S.; Brutlag, D.L. Bayesian segmentation of protein secondary structure. J. Comput. Biol. 2000, 7, 233-248.
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 233-248
-
-
Schmidler, S.C.1
Liu, J.S.2
Brutlag, D.L.3
-
67
-
-
24644438062
-
A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences
-
Li, W.; Meyer, C.A.; Liu, X.S. A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics 2005, 21 (Suppl. 1), i274-282.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Li, W.1
Meyer, C.A.2
Liu, X.S.3
-
68
-
-
0024557590
-
Stochastic models for heterogeneous DNA sequences
-
Churchill, G.A. Stochastic models for heterogeneous DNA sequences. B. Math. Biol. 1989, 51, 79-94.
-
(1989)
B. Math. Biol.
, vol.51
, pp. 79-94
-
-
Churchill, G.A.1
-
69
-
-
0028181441
-
Hidden Markov-Models in Computational Biology: Applications to Protein Modeling
-
Krogh, A.; Brown, M.; Mian, I.S.; Sjolander, K.; Haussler, D. Hidden Markov-Models in Computational Biology: Applications to Protein Modeling. J. Mol. Biol. 1994, 235, 1501-1531.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1501-1531
-
-
Krogh, A.1
Brown, M.2
Mian, I.S.3
Sjolander, K.4
Haussler, D.5
-
70
-
-
0027944605
-
A Hidden Markov Model That Finds Genes in Escherichia-Coli Dna
-
Krogh, A.; Mian, I.S.; Haussler, D. A Hidden Markov Model That Finds Genes in Escherichia-Coli Dna. Nucleic Acids Res. 1994, 22, 4768-4778.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4768-4778
-
-
Krogh, A.1
Mian, I.S.2
Haussler, D.3
-
71
-
-
0028011075
-
Hidden Markov models of biological primary sequence information
-
Baldi, P.; Chauvin, Y.; Hunkapiller, T.; McClure, M.A. Hidden Markov models of biological primary sequence information. Proc. Natl. Acad. Sci. U. S. A. 1994, 91, 1059-1063.
-
(1994)
Proc. Natl. Acad. Sci. U. S. A.
, vol.91
, pp. 1059-1063
-
-
Baldi, P.1
Chauvin, Y.2
Hunkapiller, T.3
McClure, M.A.4
-
72
-
-
0003516147
-
-
Cambridge University Press: Cambridge, UK
-
Durbin, R.L.; Eddy, S.R.; Krogh, A.; Mitchison, G. Biological sequence analysis: probabilistic models of proteins and nucleic acids; Cambridge University Press: Cambridge, UK, 1999.
-
(1999)
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
-
-
Durbin, R.L.1
Eddy, S.R.2
Krogh, A.3
Mitchison, G.4
-
73
-
-
33846913192
-
Operon prediction for sequenced bacterial genomes without experimental information
-
Bergman, N.H.; Passalacqua, K.D.; Hanna, P.C.; Qin, Z.S. Operon prediction for sequenced bacterial genomes without experimental information. Appl. Environ. Microb. 2007, 73, 846-854.
-
(2007)
Appl. Environ. Microb.
, vol.73
, pp. 846-854
-
-
Bergman, N.H.1
Passalacqua, K.D.2
Hanna, P.C.3
Qin, Z.S.4
-
75
-
-
0000803318
-
Construction of multilocus genetic linkage maps in humans
-
Lander, E.S.; Green, P. Construction of multilocus genetic linkage maps in humans. Proc. Natl. Acad. Sci. U. S. A. 1987, 84, 2363-2367.
-
(1987)
Proc. Natl. Acad. Sci. U. S. A.
, vol.84
, pp. 2363-2367
-
-
Lander, E.S.1
Green, P.2
-
76
-
-
0024610919
-
A Tutorial On Hidden Markov-Models and Selected Applications in Speech Recognition
-
Rabiner, L.R. A Tutorial On Hidden Markov-Models and Selected Applications in Speech Recognition. P. IEEE 1989, 77, 257-286.
-
(1989)
P. IEEE.
, vol.77
, pp. 257-286
-
-
Rabiner, L.R.1
-
78
-
-
70349871718
-
CEAS: Cis-regulatory element annotation system
-
Shin, H.; Liu, T.; Manrai, A.K.; Liu, X.S. CEAS: cis-regulatory element annotation system. Bioinformatics 2009, 25, 2605-2606.
-
(2009)
Bioinformatics
, vol.25
, pp. 2605-2606
-
-
Shin, H.1
Liu, T.2
Manrai, A.K.3
Liu, X.S.4
-
79
-
-
77955183656
-
PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci
-
Salmon-Divon, M.; Dvinge, H.; Tammoja, K.; Bertone, P. PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci. BMC Bioinformatics 2010, 11, 415.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 415
-
-
Salmon-Divon, M.1
Dvinge, H.2
Tammoja, K.3
Bertone, P.4
-
80
-
-
77951230100
-
Sole-Search: An integrated analysis program for peak detection and functional annotation using ChIP-seq data
-
Blahnik, K.R.; Dou, L.; O'Geen, H.; McPhillips, T.; Xu, X.; Cao, A.R.; Iyengar, S.; Nicolet, C.M.; Ludascher, B.; Korf, I.; et al. Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res. 2010, 38, e13.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Blahnik, K.R.1
Dou, L.2
O'Geen, H.3
McPhillips, T.4
Xu, X.5
Cao, A.R.6
Iyengar, S.7
Nicolet, C.M.8
Ludascher, B.9
Korf, I.10
-
81
-
-
0842265974
-
Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors
-
Kadonaga, J.T. Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell 2004, 116, 247-257.
-
(2004)
Cell
, vol.116
, pp. 247-257
-
-
Kadonaga, J.T.1
-
82
-
-
1842584947
-
Applied bioinformatics for the identification of regulatory elements
-
Wasserman, W.W.; Sandelin, A. Applied bioinformatics for the identification of regulatory elements. Nat. Rev.Genet. 2004, 5, 276-287.
-
(2004)
Nat. Rev.Genet.
, vol.5
, pp. 276-287
-
-
Wasserman, W.W.1
Sandelin, A.2
-
83
-
-
0027912333
-
Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy For Multiple Alignment
-
Lawrence, C.E.; Altschul, S.F.; Boguski, M.S.; Liu, J.S.; Neuwald, A.F.; Wootton, J.C. Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy For Multiple Alignment. Science 1993, 262, 208-214.
-
(1993)
Science
, vol.262
, pp. 208-214
-
-
Lawrence, C.E.1
Altschul, S.F.2
Boguski, M.S.3
Liu, J.S.4
Neuwald, A.F.5
Wootton, J.C.6
-
84
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey, T.L.; Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1994, 2, 28-36.
-
(1994)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
85
-
-
0035228215
-
BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
-
Liu, X.; Brutlag, D.L.; Liu, J.S. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput. 2001, 127-138.
-
(2001)
Pac. Symp. Biocomput.
, pp. 127-138
-
-
Liu, X.1
Brutlag, D.L.2
Liu, J.S.3
-
86
-
-
0036324753
-
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments
-
Liu, X.S.; Brutlag, D.L.; Liu, J.S. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol. 2002, 20, 835-839.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 835-839
-
-
Liu, X.S.1
Brutlag, D.L.2
Liu, J.S.3
-
87
-
-
0031787969
-
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
-
Roth, F.P.; Hughes, J.D.; Estep, P.W.; Church, G.M. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol. 1998, 16, 939-945.
-
(1998)
Nat. Biotechnol.
, vol.16
, pp. 939-945
-
-
Roth, F.P.1
Hughes, J.D.2
Estep, P.W.3
Church, G.M.4
-
88
-
-
0034730161
-
Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis
-
Bussemaker, H.J.; Li, H.; Siggia, E.D. Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 10096-10100.
-
(2000)
Proc. Natl. Acad. Sci. U. S. A.
, vol.97
, pp. 10096-10100
-
-
Bussemaker, H.J.1
Li, H.2
Siggia, E.D.3
-
89
-
-
0000133199
-
Identifying protein-binding sites from unaligned DNA fragments
-
Stormo, G.D.; Hartzell III, G.W. Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl. Acad. Sci. U. S. A. 1989, 86, 1183-1187.
-
(1989)
Proc. Natl. Acad. Sci. U. S. A.
, vol.86
, pp. 1183-1187
-
-
Stormo, G.D.1
Hartzell III, G.W.2
-
90
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
Tompa, M.; Li, N.; Bailey, T.L.; Church, G.M.; De Moor, B.; Eskin, E.; Favorov, A.V.; Frith, M.C.; Fu, Y.; Kent, W.J.; et al. Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol. 2005, 23, 137-144.
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 137-144
-
-
Tompa, M.1
Li, N.2
Bailey, T.L.3
Church, G.M.4
de Moor, B.5
Eskin, E.6
Favorov, A.V.7
Frith, M.C.8
Fu, Y.9
Kent, W.J.10
-
91
-
-
0035135420
-
Regulatory element detection using correlation with expression
-
Bussemaker, H.J.; Li, H.; Siggia, E.D. Regulatory element detection using correlation with expression. Nat. Genet. 2001, 27, 167-171.
-
(2001)
Nat. Genet.
, vol.27
, pp. 167-171
-
-
Bussemaker, H.J.1
Li, H.2
Siggia, E.D.3
-
92
-
-
0037453009
-
Integrating regulatory motif discovery and genome-wide expression analysis
-
Conlon, E.M.; Liu, X.S.; Lieb, J.D.; Liu, J.S. Integrating regulatory motif discovery and genome-wide expression analysis. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 3339-3344.
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 3339-3344
-
-
Conlon, E.M.1
Liu, X.S.2
Lieb, J.D.3
Liu, J.S.4
-
93
-
-
37249081604
-
Integrating quantitative information from ChIP-chip experiments into motif finding
-
Shim, H.; Keles, S. Integrating quantitative information from ChIP-chip experiments into motif finding. Biostatistics 2008, 9, 51-65.
-
(2008)
Biostatistics
, vol.9
, pp. 51-65
-
-
Shim, H.1
Keles, S.2
-
94
-
-
67649866313
-
Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data
-
Choi, H.; Nesvizhskii, A.I.; Ghosh, D.; Qin, Z.S. Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. Bioinformatics 2009, 25, 1715-1721.
-
(2009)
Bioinformatics
, vol.25
, pp. 1715-1721
-
-
Choi, H.1
Nesvizhskii, A.I.2
Ghosh, D.3
Qin, Z.S.4
-
95
-
-
53649101617
-
What would you do if you could sequence everything?
-
Kahvejian, A.; Quackenbush, J.; Thompson, J.F. What would you do if you could sequence everything? Nat. Biotechnol. 2008, 26, 1125-1133.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1125-1133
-
-
Kahvejian, A.1
Quackenbush, J.2
Thompson, J.F.3
-
96
-
-
52649157765
-
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
-
Dohm, J.C.; Lottaz, C.; Borodina, T.; Himmelbauer, H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 2008, 36, e105.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Dohm, J.C.1
Lottaz, C.2
Borodina, T.3
Himmelbauer, H.4
-
97
-
-
12844260822
-
A modified false discovery rate multiple-comparisons procedure for discrete data, applied to human immunodeficiency virus genetics
-
Gilbert, P.B. A modified false discovery rate multiple-comparisons procedure for discrete data, applied to human immunodeficiency virus genetics. J. Roy. Stat. Soc. C App. 2005, 54, 143-158.
-
(2005)
J. Roy. Stat. Soc. C App.
, vol.54
, pp. 143-158
-
-
Gilbert, P.B.1
-
98
-
-
77951286626
-
Discrete nonparametric algorithms for outlier detection with genomic data
-
Ghosh, D. Discrete nonparametric algorithms for outlier detection with genomic data. J. Biopharm. Stat. 2010, 20, 193-208.
-
(2010)
J. Biopharm. Stat.
, vol.20
, pp. 193-208
-
-
Ghosh, D.1
-
99
-
-
33747828250
-
Robust estimation of the false discovery rate
-
Pounds, S.; Cheng, C. Robust estimation of the false discovery rate. Bioinformatics 2006, 22, 1979-1987.
-
(2006)
Bioinformatics
, vol.22
, pp. 1979-1987
-
-
Pounds, S.1
Cheng, C.2
-
100
-
-
79952077182
-
Detecting outlier genes from high-dimensional data: A fuzzy approach
-
in press
-
Ghosh, D. Detecting outlier genes from high-dimensional data: a fuzzy approach. Int. J. Syst. Synth. Biol. 2010, in press.
-
(2010)
Int. J. Syst. Synth. Biol.
-
-
Ghosh, D.1
-
101
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A.; Tamayo, P.; Mootha, V.K.; Mukherjee, S.; Ebert, B.L.; Gillette, M.A.; Paulovich, A.; Pomeroy, S.L.; Golub, T.R.; Lander, E.S.; et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 15545-15550.
-
(2005)
Proc. Natl. Acad. Sci. U. S. A.
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
-
102
-
-
0038054341
-
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
-
Mootha, V.K.; Lindgren, C.M.; Eriksson, K.F.; Subramanian, A.; Sihag, S.; Lehar, J.; Puigserver, P.; Carlsson, E.; Ridderstrale, M.; Laurila, E.; et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 2003, 34, 267-273.
-
(2003)
Nat. Genet.
, vol.34
, pp. 267-273
-
-
Mootha, V.K.1
Lindgren, C.M.2
Eriksson, K.F.3
Subramanian, A.4
Sihag, S.5
Lehar, J.6
Puigserver, P.7
Carlsson, E.8
Ridderstrale, M.9
Laurila, E.10
-
103
-
-
63449107173
-
A general modular framework for gene set enrichment analysis
-
Ackermann, M.; Strimmer, K. A general modular framework for gene set enrichment analysis. BMC Bioinformatics 2009, 10, 47.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 47
-
-
Ackermann, M.1
Strimmer, K.2
-
104
-
-
65649126066
-
Transcript length bias in RNA-seq data confounds systems biology
-
Oshlack, A.; Wakefield, M.J. Transcript length bias in RNA-seq data confounds systems biology. Biol. Direct 2009, 4, 14.
-
(2009)
Biol. Direct.
, vol.4
, pp. 14
-
-
Oshlack, A.1
Wakefield, M.J.2
-
105
-
-
77953212372
-
Gene ontology analysis for RNA-seq: Accounting for selection bias
-
Young, M.D.; Wakefield, M.J.; Smyth, G.K.; Oshlack, A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010, 11, R14.
-
(2010)
Genome Biol
, vol.11
-
-
Young, M.D.1
Wakefield, M.J.2
Smyth, G.K.3
Oshlack, A.4
-
106
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell, C.; Pachter, L.; Salzberg, S.L. 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
-
107
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C.; Williams, B.A.; Pertea, G.; Mortazavi, A.; Kwan, G.; van Baren, M.J.; Salzberg, S.L.; Wold, B.J.; 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
-
108
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman, M.; Garber, M.; Levin, J.Z.; Donaghey, J.; Robinson, J.; Adiconis, X.; Fan, L.; Koziol, M.J.; Gnirke, A.; Nusbaum, C.; et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 2010, 28, 503-510.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 503-510
-
-
Guttman, M.1
Garber, M.2
Levin, J.Z.3
Donaghey, J.4
Robinson, J.5
Adiconis, X.6
Fan, L.7
Koziol, M.J.8
Gnirke, A.9
Nusbaum, C.10
-
109
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
-
Chen, X.; Xu, H.; Yuan, P.; Fang, F.; Huss, M.; Vega, V.B.; Wong, E.; Orlov, Y.L.; Zhang, W.; Jiang, J.; et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133, 1106-1117.
-
(2008)
Cell
, vol.133
, pp. 1106-1117
-
-
Chen, X.1
Xu, H.2
Yuan, P.3
Fang, F.4
Huss, M.5
Vega, V.B.6
Wong, E.7
Orlov, Y.L.8
Zhang, W.9
Jiang, J.10
-
110
-
-
0023988195
-
Genomic mapping by fingerprinting random clones: A mathematical analysis
-
Lander, E.S.; Waterman, M.S. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 1988, 2, 231-239.
-
(1988)
Genomics
, vol.2
, pp. 231-239
-
-
Lander, E.S.1
Waterman, M.S.2
-
111
-
-
45749155981
-
Aspects of coverage in medical DNA sequencing
-
Wendl, M.C.; Wilson, R.K. Aspects of coverage in medical DNA sequencing. BMC Bioinformatics 2008, 9, 239.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 239
-
-
Wendl, M.C.1
Wilson, R.K.2
-
112
-
-
24644462173
-
Accurate multiplex polony sequencing of an evolved bacterial genome
-
Shendure, J.; Porreca, G.J.; Reppas, N.B.; Lin, X.; McCutcheon, J.P.; Rosenbaum, A.M.; Wang, M.D.; Zhang, K.; Mitra, R.D.; Church, G.M. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005, 309, 1728-1732.
-
(2005)
Science
, vol.309
, pp. 1728-1732
-
-
Shendure, J.1
Porreca, G.J.2
Reppas, N.B.3
Lin, X.4
McCutcheon, J.P.5
Rosenbaum, A.M.6
Wang, M.D.7
Zhang, K.8
Mitra, R.D.9
Church, G.M.10
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