-
1
-
-
84929142779
-
Genomation: A toolkit to summarize, annotate and visualize genomic intervals
-
25417204
-
Akalin A, Franke V, Vlahoviček K, Mason CE, Schübeler D. 2015. Genomation: a toolkit to summarize, annotate and visualize genomic intervals. Bioinformatics 31:1127–1129. doi: 10.1093/bioinformatics/btu775, PMID: 25417204
-
(2015)
Bioinformatics
, vol.31
, pp. 1127-1129
-
-
Akalin, A.1
Franke, V.2
Vlahoviček, K.3
Mason, C.E.4
Schübeler, D.5
-
2
-
-
84959255113
-
Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity
-
26752769
-
Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood SA, Ponting CP, Voet T, Kelsey G, Stegle O, Reik W. 2016. Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. Nature Methods 13:229–232. doi: 10.1038/nmeth.3728, PMID: 26752769
-
(2016)
Nature Methods
, vol.13
, pp. 229-232
-
-
Angermueller, C.1
Clark, S.J.2
Lee, H.J.3
Macaulay, I.C.4
Teng, M.J.5
Hu, T.X.6
Krueger, F.7
Smallwood, S.A.8
Ponting, C.P.9
Voet, T.10
Kelsey, G.11
Stegle, O.12
Reik, W.13
-
3
-
-
84949212255
-
ATAC-seq: A method for assaying chromatin accessibility Genome-Wide
-
25559105
-
Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. 2015a. ATAC-seq: a method for assaying chromatin accessibility Genome-Wide. Current Protocols in Molecular Biology 109:21.29.1–21.29.9. doi: 10.1002/0471142727.mb2129s109, PMID: 25559105
-
(2015)
Current Protocols in Molecular Biology
, vol.109
, pp. 1-21
-
-
Buenrostro, J.D.1
Wu, B.2
Chang, H.Y.3
Greenleaf, W.J.4
-
4
-
-
84937857359
-
Single-cell chromatin accessibility reveals principles of regulatory variation
-
26083756
-
Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. 2015b. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523:486–490. doi: 10.1038/nature14590, PMID: 26083756
-
(2015)
Nature
, vol.523
, pp. 486-490
-
-
Buenrostro, J.D.1
Wu, B.2
Litzenburger, U.M.3
Ruff, D.4
Gonzales, M.L.5
Snyder, M.P.6
Chang, H.Y.7
Greenleaf, W.J.8
-
5
-
-
84873351389
-
DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing
-
23193179
-
Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W. 2013. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Research 23:341–351. doi: 10.1101/gr.142067.112, PMID: 23193179
-
(2013)
Genome Research
, vol.23
, pp. 341-351
-
-
Chen, K.1
Xi, Y.2
Pan, X.3
Li, Z.4
Kaestner, K.5
Tyler, J.6
Dent, S.7
He, X.8
Li, W.9
-
6
-
-
84930006926
-
Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing
-
25953818
-
Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J. 2015. Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348: 910–914. doi: 10.1126/science.aab1601, PMID: 25953818
-
(2015)
Science
, vol.348
, pp. 910-914
-
-
Cusanovich, D.A.1
Daza, R.2
Adey, A.3
Pliner, H.A.4
Christiansen, L.5
Gunderson, K.L.6
Steemers, F.J.7
Trapnell, C.8
Shendure, J.9
-
7
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
22955616
-
ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74. doi: 10.1038/nature11247, PMID: 22955616
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
8
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
21441907
-
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE. 2011. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473:43–49. doi: 10.1038/nature09906, PMID: 21441907
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
Kheradpour, P.2
Mikkelsen, T.S.3
Shoresh, N.4
Ward, L.D.5
Epstein, C.B.6
Zhang, X.7
Wang, L.8
Issner, R.9
Coyne, M.10
Ku, M.11
Durham, T.12
Kellis, M.13
Bernstein, B.E.14
-
9
-
-
84924601067
-
Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics
-
25732828
-
Farlik M, Sheffield NC, Nuzzo A, Datlinger P, Schönegger A, Klughammer J, Bock C. 2015. Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Reports 10:1386– 1397. doi: 10.1016/j.celrep.2015.02.001, PMID: 25732828
-
(2015)
Cell Reports
, vol.10
-
-
Farlik, M.1
Sheffield, N.C.2
Nuzzo, A.3
Datlinger, P.4
Schönegger, A.5
Klughammer, J.6
Bock, C.7
-
10
-
-
84893905629
-
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types
-
24531970
-
Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, Mildner A, Cohen N, Jung S, Tanay A, Amit I. 2014. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343:776–779. doi: 10.1126/science.1247651, PMID: 24531970
-
(2014)
Science
, vol.343
, pp. 776-779
-
-
Jaitin, D.A.1
Kenigsberg, E.2
Keren-Shaul, H.3
Elefant, N.4
Paul, F.5
Zaretsky, I.6
Mildner, A.7
Cohen, N.8
Jung, S.9
Tanay, A.10
Amit, I.11
-
11
-
-
84949227165
-
Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples
-
26605532
-
Jin W, Tang Q, Wan M, Cui K, Zhang Y, Ren G, Ni B, Sklar J, Przytycka TM, Childs R, Levens D, Zhao K. 2015. Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples. Nature 528:1– 17. doi: 10.1038/nature15740, PMID: 26605532
-
(2015)
Nature
, vol.528
-
-
Jin, W.1
Tang, Q.2
Wan, M.3
Cui, K.4
Zhang, Y.5
Ren, G.6
Ni, B.7
Sklar, J.8
Przytycka, T.M.9
Childs, R.10
Levens, D.11
Zhao, K.12
-
12
-
-
84891771466
-
The UCSC Genome browser database: 2014 update
-
24270787
-
Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, et al. 2014. The UCSC Genome browser database: 2014 update. Nucleic Acids Research 42:D764– D770. doi: 10.1093/nar/gkt1168, PMID: 24270787
-
(2014)
Nucleic Acids Research
, vol.42
-
-
Karolchik, D.1
Barber, G.P.2
Casper, J.3
Clawson, H.4
Cline, M.S.5
Diekhans, M.6
Dreszer, T.R.7
Fujita, P.A.8
Guruvadoo, L.9
Haeussler, M.10
Harte, R.A.11
Heitner, S.12
Hinrichs, A.S.13
Learned, K.14
Lee, B.T.15
Li, C.H.16
Raney, B.J.17
Rhead, B.18
Rosenbloom, K.R.19
Sloan, C.A.20
more..
-
13
-
-
84870552401
-
Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules
-
22960375
-
Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA. 2012. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Research 22:2497–2506. doi: 10.1101/gr.143008.112, PMID: 22960375
-
(2012)
Genome Research
, vol.22
, pp. 2497-2506
-
-
Kelly, T.K.1
Liu, Y.2
Lay, F.D.3
Liang, G.4
Berman, B.P.5
Jones, P.A.6
-
14
-
-
0036079158
-
The human genome browser at UCSC
-
12045153
-
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Research 12:996–1006. doi: 10.1101/gr.229102, PMID: 12045153
-
(2002)
Genome Research
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
Haussler, D.7
-
15
-
-
33847049022
-
Single-molecule and population probing of chromatin structure using DNA methyltransferases
-
17309843
-
Kilgore JA, Hoose SA, Gustafson TL, Porter W, Kladde MP. 2007. Single-molecule and population probing of chromatin structure using DNA methyltransferases. Methods 41:320–332. doi: 10.1016/j.ymeth.2006.08.008, PMID: 17309843
-
(2007)
Methods
, vol.41
, pp. 320-332
-
-
Kilgore, J.A.1
Hoose, S.A.2
Gustafson, T.L.3
Porter, W.4
Kladde, M.P.5
-
16
-
-
84856498057
-
DNA methylome analysis using short bisulfite sequencing data
-
22290186
-
Krueger F, Kreck B, Franke A, Andrews SR. 2012. DNA methylome analysis using short bisulfite sequencing data. Nature Methods 9:145–151. doi: 10.1038/nmeth.1828, PMID: 22290186
-
(2012)
Nature Methods
, vol.9
, pp. 145-151
-
-
Krueger, F.1
Kreck, B.2
Franke, A.3
Andrews, S.R.4
-
17
-
-
84859210032
-
Fast gapped-read alignment with bowtie 2
-
22388286
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with bowtie 2. Nature Methods 9:357–359. doi: 10.1038/nmeth.1923, PMID: 22388286
-
(2012)
Nature Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
18
-
-
68549104404
-
The sequence alignment/Map format and SAMtools
-
19505943
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. doi: 10.1093/bioinformatics/btp352, PMID: 19505943
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
19
-
-
84929684999
-
Highly parallel Genome-wide expression profiling of individual cells using Nanoliter Droplets
-
26000488
-
Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, Trombetta JJ, Weitz DA, Sanes JR, Shalek AK, Regev A, McCarroll SA. 2015. Highly parallel Genome-wide expression profiling of individual cells using Nanoliter Droplets. Cell 161:1202–1214. doi: 10.1016/j.cell.2015.05.002, PMID: 26000488
-
(2015)
Cell
, vol.161
, pp. 1202-1214
-
-
Macosko, E.Z.1
Basu, A.2
Satija, R.3
Nemesh, J.4
Shekhar, K.5
Goldman, M.6
Tirosh, I.7
Bialas, A.R.8
Kamitaki, N.9
Martersteck, E.M.10
Trombetta, J.J.11
Weitz, D.A.12
Sanes, J.R.13
Shalek, A.K.14
Regev, A.15
McCarroll, S.A.16
-
20
-
-
84938401651
-
Taking stock of regulatory variation
-
27135686
-
Maurano MT, Stamatoyannopoulos JA. 2015. Taking stock of regulatory variation. Cell Systems 1:18–21. doi: 10. 1016/j.cels.2015.07.011, PMID: 27135686
-
(2015)
Cell Systems
, vol.1
, pp. 18-21
-
-
Maurano, M.T.1
Stamatoyannopoulos, J.A.2
-
21
-
-
75949101193
-
Methylation-sensitive single-molecule analysis of chromatin structure
-
Chapter 21:Unit 21.17.1–21.1716, 20069538
-
Miranda TB, Kelly TK, Bouazoune K, Jones PA. 2010. Methylation-sensitive single-molecule analysis of chromatin structure. Current Protocols in Molecular Biology Chapter 21:Unit 21.17.1–21.1716. doi: 10.1002/0471142727.mb2117s89, PMID: 20069538
-
(2010)
Current Protocols in Molecular Biology
-
-
Miranda, T.B.1
Kelly, T.K.2
Bouazoune, K.3
Jones, P.A.4
-
22
-
-
84865708757
-
An expansive human regulatory lexicon encoded in transcription factor footprints
-
22955618
-
Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, et al. 2012. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489:83–90. doi: 10.1038/nature11212, PMID: 22955618
-
(2012)
Nature
, vol.489
, pp. 83-90
-
-
Neph, S.1
Vierstra, J.2
Stergachis, A.B.3
Reynolds, A.P.4
Haugen, E.5
Vernot, B.6
Thurman, R.E.7
John, S.8
Sandstrom, R.9
Johnson, A.K.10
Maurano, M.T.11
Humbert, R.12
Rynes, E.13
Wang, H.14
Vong, S.15
Lee, K.16
Bates, D.17
Diegel, M.18
Roach, V.19
Dunn, D.20
more..
-
24
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
20110278
-
Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842. doi: 10.1093/bioinformatics/btq033, PMID: 20110278
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
26
-
-
84946545109
-
Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state
-
26458175
-
Rotem A, Ram O, Shoresh N, Sperling RA, Goren A, Weitz DA, Bernstein BE. 2015. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nature Biotechnology 33:1165–1172. doi: 10.1038/nbt.3383, PMID: 26458175
-
(2015)
Nature Biotechnology
, vol.33
, pp. 1165-1172
-
-
Rotem, A.1
Ram, O.2
Shoresh, N.3
Sperling, R.A.4
Goren, A.5
Weitz, D.A.6
Bernstein, B.E.7
-
27
-
-
39749145198
-
Dynamic regulation of nucleosome positioning in the human genome
-
1832 9373
-
Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. 2008. Dynamic regulation of nucleosome positioning in the human genome. Cell 132:887–898. doi: 10.1016/j.cell.2008.02.022, PMID: 1832 9373
-
(2008)
Cell
, vol.132
, pp. 887-898
-
-
Schones, D.E.1
Cui, K.2
Cuddapah, S.3
Roh, T.Y.4
Barski, A.5
Wang, Z.6
Wei, G.7
Zhao, K.8
-
28
-
-
84922621952
-
Function and information content of DNA methylation
-
25592537
-
Schübeler D. 2015. Function and information content of DNA methylation. Nature 517:321–326. doi: 10.1038/nature14192, PMID: 25592537
-
(2015)
Nature
, vol.517
, pp. 321-326
-
-
Schübeler, D.1
-
29
-
-
84903185013
-
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
-
24919153
-
Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, Ding R, Raychowdhury R, Friedman N, Hacohen N, Park H, et al. 2014. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature 510:263–269. doi: 10.1038/nature13437, PMID: 24919153
-
(2014)
Nature
, vol.510
, pp. 263-269
-
-
Shalek, A.K.1
Satija, R.2
Shuga, J.3
Trombetta, J.J.4
Gennert, D.5
Lu, D.6
Chen, P.7
Gertner, R.S.8
Gaublomme, J.T.9
Yosef, N.10
Schwartz, S.11
Fowler, B.12
Weaver, S.13
Wang, J.14
Wang, X.15
Ding, R.16
Raychowdhury, R.17
Friedman, N.18
Hacohen, N.19
Park, H.20
more..
-
30
-
-
84902596852
-
Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity
-
24889621
-
Small EC, Xi L, Wang JP, Widom J, Licht JD. 2014. Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity. PNAS 111:E2462–E2471. doi: 10.1073/pnas.1400517111, PMID: 24889621
-
(2014)
PNAS
, vol.111
, pp. E2462-E2471
-
-
Small, E.C.1
Xi, L.2
Wang, J.P.3
Widom, J.4
Licht, J.D.5
-
31
-
-
84905405443
-
Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity
-
25042786
-
Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, Andrews SR, Stegle O, Reik W, Kelsey G. 2014. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nature Methods 11:817–820. doi: 10.1038/nmeth.3035, PMID: 25042786
-
(2014)
Nature Methods
, vol.11
, pp. 817-820
-
-
Smallwood, S.A.1
Lee, H.J.2
Angermueller, C.3
Krueger, F.4
Saadeh, H.5
Peat, J.6
Andrews, S.R.7
Stegle, O.8
Reik, W.9
Kelsey, G.10
-
32
-
-
84355163093
-
DNA-binding factors shape the mouse methylome at distal regulatory regions
-
22170606
-
Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D. 2011. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480:1–7. doi: 10.1038/nature10716, PMID: 22170606
-
(2011)
Nature
, vol.480
, pp. 1-7
-
-
Stadler, M.B.1
Murr, R.2
Burger, L.3
Ivanek, R.4
Lienert, F.5
Schöler, A.6
Van Nimwegen, E.7
Wirbelauer, C.8
Oakeley, E.J.9
Gaidatzis, D.10
Tiwari, V.K.11
Schübeler, D.12
-
33
-
-
84907196865
-
Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in Cancer
-
24916973
-
Taberlay PC, Statham AL, Kelly TK, Clark SJ, Jones PA. 2014. Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in Cancer. Genome Research 24:1421–1432. doi: 10.1101/gr.163485.113, PMID: 24916973
-
(2014)
Genome Research
, vol.24
, pp. 1421-1432
-
-
Taberlay, P.C.1
Statham, A.L.2
Kelly, T.K.3
Clark, S.J.4
Jones, P.A.5
-
35
-
-
84900529199
-
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
-
24739965
-
Treutlein B, Brownfield DG, Wu AR, Neff NF, Mantalas GL, Espinoza FH, Desai TJ, Krasnow MA, Quake SR. 2014. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 509: 371–375. doi: 10.1038/nature13173, PMID: 24739965
-
(2014)
Nature
, vol.509
, pp. 371-375
-
-
Treutlein, B.1
Brownfield, D.G.2
Ar, W.3
Neff, N.F.4
Mantalas, G.L.5
Espinoza, F.H.6
Desai, T.J.7
Krasnow, M.A.8
Quake, S.R.9
-
36
-
-
79959557189
-
Determinants of nucleosome organization in primary human cells
-
21602827
-
Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. 2011. Determinants of nucleosome organization in primary human cells. Nature 474:516–520. doi: 10.1038/nature10002, PMID: 21602827
-
(2011)
Nature
, vol.474
, pp. 516-520
-
-
Valouev, A.1
Johnson, S.M.2
Boyd, S.D.3
Smith, C.L.4
Fire, A.Z.5
Sidow, A.6
-
38
-
-
84909944591
-
-
New York, Springer Science & Business Media
-
Wickham H. 2009. Ggplot2. New York, Springer Science & Business Media.
-
(2009)
Ggplot2
-
-
Wickham, H.1
-
39
-
-
84923382398
-
Dissecting neural differentiation regulatory networks through epigenetic footprinting
-
25533951
-
Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cacchiarelli D, Tsankov AM, Epstein C, Rinn JL, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, et al. 2015. Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature 518:355–359. doi: 10.1038/nature13990, PMID: 25533951
-
(2015)
Nature
, vol.518
, pp. 355-359
-
-
Ziller, M.J.1
Edri, R.2
Yaffe, Y.3
Donaghey, J.4
Pop, R.5
Mallard, W.6
Issner, R.7
Gifford, C.A.8
Goren, A.9
Xing, J.10
Gu, H.11
Cacchiarelli, D.12
Tsankov, A.M.13
Epstein, C.14
Rinn, J.L.15
Mikkelsen, T.S.16
Kohlbacher, O.17
Gnirke, A.18
Bernstein, B.E.19
Elkabetz, Y.20
more..
|