-
1
-
-
84888877924
-
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
-
COI: 1:CAS:528:DC%2BC3sXhsFOiu7jO
-
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013)
-
(2013)
Nat. Methods
, vol.10
, pp. 1213-1218
-
-
Buenrostro, J.D.1
Giresi, P.G.2
Zaba, L.C.3
Chang, H.Y.4
Greenleaf, W.J.5
-
2
-
-
84930006926
-
Epigenetics. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
-
COI: 1:CAS:528:DC%2BC2MXosFaksLk%3D
-
Cusanovich, D. A. et al. Epigenetics. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348, 910–914 (2015)
-
(2015)
Science
, vol.348
, pp. 910-914
-
-
Cusanovich, D.A.1
-
3
-
-
84937857359
-
Single-cell chromatin accessibility reveals principles of regulatory variation
-
COI: 1:CAS:528:DC%2BC2MXhtFyltLrN
-
Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486–490 (2015)
-
(2015)
Nature
, vol.523
, pp. 486-490
-
-
Buenrostro, J.D.1
-
4
-
-
85040463710
-
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain
-
COI: 1:CAS:528:DC%2BC2sXhvFGmurrM
-
Lake, B. B. et al. Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. Nat. Biotechnol. 36, 70–80 (2018)
-
(2018)
Nat. Biotechnol.
, vol.36
, pp. 70-80
-
-
Lake, B.B.1
-
5
-
-
85044334985
-
The cis-regulatory dynamics of embryonic development at single-cell resolution
-
COI: 1:CAS:528:DC%2BC1cXksFegu7g%3D
-
Cusanovich, D. A. et al. The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature 555, 538–542 (2018)
-
(2018)
Nature
, vol.555
, pp. 538-542
-
-
Cusanovich, D.A.1
-
6
-
-
84982146199
-
Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution
-
Ryan Corces, M. et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat. Genet. 48, 1193–1203 (2016)
-
(2016)
Nat. Genet.
, vol.48
, pp. 1193-1203
-
-
Ryan Corces, M.1
-
7
-
-
85052990879
-
High-throughput chromatin accessibility profiling at single-cell resolution
-
Mezger, A. et al. High-throughput chromatin accessibility profiling at single-cell resolution. Nat. Commun. 9, 3647 (2018)
-
(2018)
Nat. Commun.
, vol.9
-
-
Mezger, A.1
-
9
-
-
85041914298
-
Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation
-
COI: 1:CAS:528:DC%2BC1cXltVyhsLY%3D
-
Preissl, S. et al. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat. Neurosci. 21, 432–439 (2018)
-
(2018)
Nat. Neurosci.
, vol.21
, pp. 432-439
-
-
Preissl, S.1
-
10
-
-
84922537404
-
Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing
-
COI: 1:CAS:528:DC%2BC2cXhslOisrnN
-
Amini, S. et al. Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat. Genet. 46, 1343–1349 (2014)
-
(2014)
Nat. Genet.
, vol.46
, pp. 1343-1349
-
-
Amini, S.1
-
11
-
-
84913593681
-
Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
-
COI: 1:CAS:528:DC%2BC2cXitVOls7%2FF
-
Picelli, S. et al. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res. 24, 2033–2040 (2014)
-
(2014)
Genome Res.
, vol.24
, pp. 2033-2040
-
-
Picelli, S.1
-
12
-
-
0033987603
-
Insertional transposon mutagenesis by electroporation of released Tn5 transposition complexes
-
COI: 1:CAS:528:DC%2BD3cXjvVegtA%3D%3D
-
Goryshin, I. Y., Jendrisak, J., Hoffman, L. M., Meis, R. & Reznikoff, W. S. Insertional transposon mutagenesis by electroporation of released Tn5 transposition complexes. Nat. Biotechnol. 18, 97–100 (2000)
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 97-100
-
-
Goryshin, I.Y.1
Jendrisak, J.2
Hoffman, L.M.3
Meis, R.4
Reznikoff, W.S.5
-
13
-
-
85030994641
-
An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues
-
COI: 1:CAS:528:DC%2BC2sXhtl2gtL7F
-
Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods 14, 959–962 (2017)
-
(2017)
Nat. Methods
, vol.14
, pp. 959-962
-
-
Corces, M.R.1
-
14
-
-
0029061907
-
A simple ‘universal’ DNA extraction procedure using SDS and proteinase K is compatible with direct PCR amplification
-
COI: 1:CAS:528:DyaK2MXmtlOqsrY%3D
-
Goldenberger, D., Perschil, I., Ritzler, M. & Altwegg, M. A simple ‘universal’ DNA extraction procedure using SDS and proteinase K is compatible with direct PCR amplification. PCR Methods Appl. 4, 368–370 (1995)
-
(1995)
PCR Methods Appl.
, vol.4
, pp. 368-370
-
-
Goldenberger, D.1
Perschil, I.2
Ritzler, M.3
Altwegg, M.4
-
17
-
-
52649097448
-
The Immunological Genome Project: networks of gene expression in immune cells
-
COI: 1:CAS:528:DC%2BD1cXhtFeit7zE
-
Heng, T. S. P. & Painter, M. W., Immunological Genome Project Consortium. The Immunological Genome Project: networks of gene expression in immune cells. Nat. Immunol. 9, 1091–1094 (2008)
-
(2008)
Nat. Immunol.
, vol.9
, pp. 1091-1094
-
-
Heng, T.S.P.1
Painter, M.W.2
-
18
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008)
-
(2008)
Genome Biol.
, vol.9
-
-
Zhang, Y.1
-
20
-
-
33750442190
-
Normal structure, function, and histology of the spleen
-
Cesta, M. F. Normal structure, function, and histology of the spleen. Toxicol. Pathol. 34, 455–465 (2006)
-
(2006)
Toxicol. Pathol.
, vol.34
, pp. 455-465
-
-
Cesta, M.F.1
-
21
-
-
34548583274
-
A tutorial on spectral clustering
-
von Luxburg, U. A tutorial on spectral clustering. Stat. Comput. 17, 395–416 (2007)
-
(2007)
Stat. Comput.
, vol.17
, pp. 395-416
-
-
von Luxburg, U.1
-
22
-
-
84959346645
-
Inducible chromatin priming is associated with the establishment of immunological memory in T cells
-
COI: 1:CAS:528:DC%2BC28XhtFSqtbs%3D
-
Bevington, S. L. et al. Inducible chromatin priming is associated with the establishment of immunological memory in T cells. EMBO J. 35, 515–535 (2016)
-
(2016)
EMBO J.
, vol.35
, pp. 515-535
-
-
Bevington, S.L.1
-
23
-
-
84866975037
-
Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification
-
COI: 1:CAS:528:DC%2BC38XhsValt73N
-
Samstein, R. M. et al. Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification. Cell 151, 153–166 (2012)
-
(2012)
Cell
, vol.151
, pp. 153-166
-
-
Samstein, R.M.1
-
24
-
-
25844475244
-
IL-18-induced CD83+CCR7+ NK helper cells
-
COI: 1:CAS:528:DC%2BD2MXhtVygt7rN
-
Mailliard, R. B. et al. IL-18-induced CD83+CCR7+ NK helper cells. J. Exp. Med. 202, 941–953 (2005)
-
(2005)
J. Exp. Med.
, vol.202
, pp. 941-953
-
-
Mailliard, R.B.1
-
25
-
-
0028968389
-
Human blood dendritic cells selectively express CD83, a member of the immunoglobulin superfamily
-
COI: 1:CAS:528:DyaK2MXkvFOrtLw%3D, PID: 7706722
-
Zhou, L. J. & Tedder, T. F. Human blood dendritic cells selectively express CD83, a member of the immunoglobulin superfamily. J. Immunol. 154, 3821–3835 (1995)
-
(1995)
J. Immunol.
, vol.154
, pp. 3821-3835
-
-
Zhou, L.J.1
Tedder, T.F.2
-
26
-
-
31144449386
-
CD27 dissects mature NK cells into two subsets with distinct responsiveness and migratory capacity
-
COI: 1:CAS:528:DC%2BD28XlsFygtg%3D%3D
-
Hayakawa, Y. & Smyth, M. J. CD27 dissects mature NK cells into two subsets with distinct responsiveness and migratory capacity. J. Immunol. 176, 1517–1524 (2006)
-
(2006)
J. Immunol.
, vol.176
, pp. 1517-1524
-
-
Hayakawa, Y.1
Smyth, M.J.2
-
27
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
COI: 1:CAS:528:DC%2BC3cXns1SlsLc%3D
-
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010)
-
(2010)
Mol. Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
-
28
-
-
84899986363
-
Transcriptional regulation in the immune system: a status report
-
COI: 1:CAS:528:DC%2BC2cXltl2htLk%3D
-
Smale, S. T. Transcriptional regulation in the immune system: a status report. Trends Immunol. 35, 190–194 (2014)
-
(2014)
Trends Immunol.
, vol.35
, pp. 190-194
-
-
Smale, S.T.1
-
29
-
-
84977471548
-
T-bet and eomesodermin in NK cell development, maturation, and function
-
Simonetta, F., Pradier, A. & Roosnek, E. T-bet and eomesodermin in NK cell development, maturation, and function. Front. Immunol. 7, 241 (2016)
-
(2016)
Front. Immunol.
, vol.7
, pp. 241
-
-
Simonetta, F.1
Pradier, A.2
Roosnek, E.3
-
30
-
-
30044440799
-
Effector and memory CD8+ T cell fate coupled by T-bet and eomesodermin
-
COI: 1:CAS:528:DC%2BD2MXhtlShurrM
-
Intlekofer, A. M. et al. Effector and memory CD8+ T cell fate coupled by T-bet and eomesodermin. Nat. Immunol. 6, 1236–1244 (2005)
-
(2005)
Nat. Immunol.
, vol.6
, pp. 1236-1244
-
-
Intlekofer, A.M.1
-
31
-
-
0036580887
-
Marginal-zone B cells
-
COI: 1:CAS:528:DC%2BD38Xjsl2rs74%3D
-
Martin, F. & Kearney, J. F. Marginal-zone B cells. Nat. Rev. Immunol. 2, 323–335 (2002)
-
(2002)
Nat. Rev. Immunol.
, vol.2
, pp. 323-335
-
-
Martin, F.1
Kearney, J.F.2
-
32
-
-
84949227165
-
Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples
-
COI: 1:CAS:528:DC%2BC2MXhvFagtbzK, PID: 26605532
-
Jin, W. et al. Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples. Nature 528, 142–146 (2015)
-
(2015)
Nature
, vol.528
, pp. 142-146
-
-
Jin, W.1
-
33
-
-
85054652069
-
Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing
-
PID: 30487604
-
Lai, B. et al. Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing. Nature 562, 281–285 (2018)
-
(2018)
Nature
-
-
Lai, B.1
-
34
-
-
85022345215
-
Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells
-
Pott, S. Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells. elife 6, e23203 (2017)
-
(2017)
elife
, vol.6
-
-
Pott, S.1
-
35
-
-
85042554322
-
scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells
-
Clark, S. J. et al. scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nat. Commun. 9, 781 (2018)
-
(2018)
Nat. Commun.
, vol.9
-
-
Clark, S.J.1
-
36
-
-
85053830755
-
A single-cell atlas of in vivo mammalian chromatin accessibility
-
PID: 30078704
-
Cusanovich, D. A. et al. A single-cell atlas of in vivo mammalian chromatin accessibility. Cell 174, 1309–1324 (2018)
-
(2018)
Cell
-
-
Cusanovich, D.A.1
-
37
-
-
85053831649
-
Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data
-
PID: 30078726
-
Pliner, H. A. et al. Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data. Mol. Cell 71, 858–871 (2018)
-
(2018)
Mol. Cell
-
-
Pliner, H.A.1
-
38
-
-
85054154765
-
Joint profiling of chromatin accessibility and gene expression in thousands of single cells
-
COI: 1:CAS:528:DC%2BC1cXhslOrur3I
-
Cao, J. et al. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science 361, 1380–1385 (2018)
-
(2018)
Science
, vol.361
, pp. 1380-1385
-
-
Cao, J.1
-
40
-
-
84926519013
-
HISAT: a fast spliced aligner with low memory requirements
-
COI: 1:CAS:528:DC%2BC2MXjvFOnsL0%3D
-
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015)
-
(2015)
Nat. Methods
, vol.12
, pp. 357-360
-
-
Kim, D.1
Langmead, B.2
Salzberg, S.L.3
-
41
-
-
84867306721
-
Snakemake—a scalable bioinformatics workflow engine
-
Köster, J. & Rahmann, S. Snakemake—a scalable bioinformatics workflow engine. Bioinformatics 28, 2520–2522 (2012)
-
(2012)
Bioinformatics
, vol.28
, pp. 2520-2522
-
-
Köster, J.1
Rahmann, S.2
-
42
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10–12 (2011)
-
(2011)
EMBnet. J.
, vol.17
, pp. 10-12
-
-
Martin, M.1
-
43
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009)
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
44
-
-
77951770756
-
BEDTools: a flexible suite of utilities for comparing genomic features
-
COI: 1:CAS:528:DC%2BC3cXivFGkurc%3D
-
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010)
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
45
-
-
80555140075
-
Scikit-learn: machine learning in Python
-
Pedregosa, F. et al. Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011)
-
(2011)
J. Mach. Learn. Res.
, vol.12
, pp. 2825-2830
-
-
Pedregosa, F.1
|