-
1
-
-
84869457261
-
The expanding scope of DNA sequencing
-
23138308 PubMed Central PMCID: PMC4149750
-
Shendure J, Lieberman Aiden E. The expanding scope of DNA sequencing. Nature biotechnology. 2012; 30(11):1084-94. PubMed Central PMCID: PMC4149750. doi: 10.1038/nbt.2421 PMID: 23138308
-
(2012)
Nature Biotechnology.
, vol.30
, Issue.11
, pp. 1084-1094
-
-
Shendure, J.1
Lieberman Aiden, E.2
-
2
-
-
80054973803
-
A high-resolution map of human evolutionary constraint using 29 mammals
-
21993624 PubMed Central PMCID: PMC3207357
-
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011; 478(7370):476-82. PubMed Central PMCID: PMC3207357. doi: 10.1038/nature10530 PMID: 21993624
-
(2011)
Nature
, vol.478
, Issue.7370
, pp. 476-482
-
-
Lindblad-Toh, K.1
Garber, M.2
Zuk, O.3
Lin, M.F.4
Parker, B.J.5
Washietl, S.6
-
3
-
-
33748675254
-
An RNA gene expressed during cortical development evolved rapidly in humans
-
16915236
-
Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, et al. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 2006; 443(7108):167-72. doi: 10.1038/nature05113 PMID: 16915236
-
(2006)
Nature
, vol.443
, Issue.7108
, pp. 167-172
-
-
Pollard, K.S.1
Salama, S.R.2
Lambert, N.3
Lambot, M.A.4
Coppens, S.5
Pedersen, J.S.6
-
4
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
17086198
-
Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature. 2006; 444(7118):499-502. doi: 10.1038/ nature05295 PMID: 17086198
-
(2006)
Nature
, vol.444
, Issue.7118
, pp. 499-502
-
-
Pennacchio, L.A.1
Ahituv, N.2
Moses, A.M.3
Prabhakar, S.4
Nobrega, M.A.5
Shoukry, M.6
-
5
-
-
84891371778
-
A genome-wide association study identifies multiple susceptibility loci for chronic lymphocytic leukemia
-
24292274
-
Speedy HE, Di Bernardo MC, Sava GP, Dyer MJ, Holroyd A, Wang Y, et al. A genome-wide association study identifies multiple susceptibility loci for chronic lymphocytic leukemia. Nature genetics. 2014; 46 (1):56-60. doi: 10.1038/ng.2843 PMID: 24292274
-
(2014)
Nature Genetics.
, vol.46
, Issue.1
, pp. 56-60
-
-
Speedy, H.E.1
Di Bernardo, M.C.2
Sava, G.P.3
Dyer, M.J.4
Holroyd, A.5
Wang, Y.6
-
6
-
-
55449120805
-
Genetic mapping in human disease
-
18988837 PubMed Central PMCID: PMC2694957
-
Altshuler D, Daly MJ, Lander ES. Genetic mapping in human disease. Science. 2008; 322(5903):881-8. PubMed Central PMCID: PMC2694957. doi: 10.1126/science.1156409 PMID: 18988837
-
(2008)
Science
, vol.322
, Issue.5903
, pp. 881-888
-
-
Altshuler, D.1
Daly, M.J.2
Lander, E.S.3
-
7
-
-
84959523025
-
Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease
-
Zmora N, Zeevi D, Korem T, Segal E, Elinav E. Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease. Cell host & microbe. 2016; 19(1):12-20.
-
(2016)
Cell Host & Microbe.
, vol.19
, Issue.1
, pp. 12-20
-
-
Zmora, N.1
Zeevi, D.2
Korem, T.3
Segal, E.4
Elinav, E.5
-
8
-
-
84947648658
-
Next-generation technologies for multiomics approaches including interactome sequencing
-
25649523 PubMed Central PMCID: PMC4306365
-
Ohashi H, Hasegawa M, Wakimoto K, Miyamoto-Sato E. Next-generation technologies for multiomics approaches including interactome sequencing. BioMed research international. 2015; 2015:104209. PubMed Central PMCID: PMC4306365. doi: 10.1155/2015/104209 PMID: 25649523
-
(2015)
BioMed Research International.
, vol.2015
, pp. 104209
-
-
Ohashi, H.1
Hasegawa, M.2
Wakimoto, K.3
Miyamoto-Sato, E.4
-
9
-
-
84893723345
-
Library preparation methods for next-generation sequencing: Tone down the bias
-
24440557
-
van Dijk EL, Jaszczyszyn Y, Thermes C. Library preparation methods for next-generation sequencing: tone down the bias. Experimental cell research. 2014; 322(1):12-20. doi: 10.1016/j.yexcr.2014.01.008 PMID: 24440557
-
(2014)
Experimental Cell Research.
, vol.322
, Issue.1
, pp. 12-20
-
-
Van Dijk, E.L.1
Jaszczyszyn, Y.2
Thermes, C.3
-
10
-
-
57049122389
-
A large genome center's improvements to the Illumina sequencing system
-
19034268 PubMed Central PMCID: PMC2610436
-
Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, et al. A large genome center's improvements to the Illumina sequencing system. Nature methods. 2008; 5(12):1005-10. PubMed Central PMCID: PMC2610436. doi: 10.1038/nmeth.1270 PMID: 19034268
-
(2008)
Nature Methods.
, vol.5
, Issue.12
, pp. 1005-1010
-
-
Quail, M.A.1
Kozarewa, I.2
Smith, F.3
Scally, A.4
Stephens, P.J.5
Durbin, R.6
-
11
-
-
84856448155
-
Optimal enzymes for amplifying sequencing libraries
-
Quail MA, Otto TD, Gu Y, Harris SR, Skelly TF, McQuillan JA, et al. Optimal enzymes for amplifying sequencing libraries. Nature methods. 2012; 9(1):10-1.
-
(2012)
Nature Methods.
, vol.9
, Issue.1
, pp. 10-11
-
-
Quail, M.A.1
Otto, T.D.2
Gu, Y.3
Harris, S.R.4
Skelly, T.F.5
McQuillan, J.A.6
-
12
-
-
84855219212
-
Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes
-
22214261 PubMed Central PMCID: PMC3312816
-
Oyola SO, Otto TD, Gu Y, Maslen G, Manske M, Campino S, et al. Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC genomics. 2012; 13:1. PubMed Central PMCID: PMC3312816. doi: 10.1186/1471-2164-13-1 PMID: 22214261
-
(2012)
BMC Genomics.
, vol.13
, pp. 1
-
-
Oyola, S.O.1
Otto, T.D.2
Gu, Y.3
Maslen, G.4
Manske, M.5
Campino, S.6
-
13
-
-
79951694175
-
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
-
21338519 PubMed Central PMCID: PMC3188800
-
Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome biology. 2011; 12(2):R18. PubMed Central PMCID: PMC3188800. doi: 10.1186/gb-2011-12-2-r18 PMID: 21338519
-
(2011)
Genome Biology.
, vol.12
, Issue.2
, pp. R18
-
-
Aird, D.1
Ross, M.G.2
Chen, W.S.3
Danielsson, M.4
Fennell, T.5
Russ, C.6
-
14
-
-
84857271408
-
Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries
-
22313406
-
Dabney J, Meyer M. Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. BioTechniques. 2012; 52(2):87-94. doi: 10.2144/000113809 PMID: 22313406
-
(2012)
BioTechniques.
, vol.52
, Issue.2
, pp. 87-94
-
-
Dabney, J.1
Meyer, M.2
-
15
-
-
78649793093
-
Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles
-
21152096 PubMed Central PMCID: PMC2994895
-
Mokry M, Hatzis P, de Bruijn E, Koster J, Versteeg R, Schuijers J, et al. Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles. PloS one. 2010; 5(11):e15092. PubMed Central PMCID: PMC2994895. doi: 10.1371/journal.pone.0015092 PMID: 21152096
-
(2010)
PloS One.
, vol.5
, Issue.11
, pp. e15092
-
-
Mokry, M.1
Hatzis, P.2
De Bruijn, E.3
Koster, J.4
Versteeg, R.5
Schuijers, J.6
-
16
-
-
0035046755
-
Reverse transcriptase template switching: A SMART approach for full-length cDNA library construction
-
11314272
-
Zhu YY, Machleder EM, Chenchik A, Li R, Siebert PD. Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. BioTechniques. 2001; 30(4):892-7. PMID: 11314272
-
(2001)
BioTechniques.
, vol.30
, Issue.4
, pp. 892-897
-
-
Zhu, Y.Y.1
Machleder, E.M.2
Chenchik, A.3
Li, R.4
Siebert, P.D.5
-
17
-
-
84864880991
-
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
-
22820318 PubMed Central PMCID: PMC3467340
-
Ramskold D, Luo S, Wang YC, Li R, Deng Q, Faridani OR, et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nature biotechnology. 2012; 30(8):777-82. PubMed Central PMCID: PMC3467340. doi: 10.1038/nbt.2282 PMID: 22820318
-
(2012)
Nature Biotechnology.
, vol.30
, Issue.8
, pp. 777-782
-
-
Ramskold, D.1
Luo, S.2
Wang, Y.C.3
Li, R.4
Deng, Q.5
Faridani, O.R.6
-
18
-
-
84864873214
-
Transcriptome sequencing of single cells with Smart-Seq
-
22871714
-
Goetz JJ, Trimarchi JM. Transcriptome sequencing of single cells with Smart-Seq. Nature biotechnology. 2012; 30(8):763-5. doi: 10.1038/nbt.2325 PMID: 22871714
-
(2012)
Nature Biotechnology.
, vol.30
, Issue.8
, pp. 763-765
-
-
Goetz, J.J.1
Trimarchi, J.M.2
-
19
-
-
0014633976
-
Incorporation of thymine into prototrophic and thymine-dependent mutants of Bacillus anthracis
-
4984854
-
Ivanovics G, Dobozy A, Pal L. Incorporation of thymine into prototrophic and thymine-dependent mutants of Bacillus anthracis. Journal of general microbiology. 1969; 59(3):337-49. doi: 10.1099/ 00221287-59-3-337 PMID: 4984854
-
(1969)
Journal of General Microbiology.
, vol.59
, Issue.3
, pp. 337-349
-
-
Ivanovics, G.1
Dobozy, A.2
Pal, L.3
-
20
-
-
84902840108
-
Technical variations in low-input RNA-seq methodologies
-
24419370 PubMed Central PMCID: PMC3890974
-
Bhargava V, Head SR, Ordoukhanian P, Mercola M, Subramaniam S. Technical variations in low-input RNA-seq methodologies. Scientific reports. 2014; 4:3678. PubMed Central PMCID: PMC3890974. doi: 10.1038/srep03678 PMID: 24419370
-
(2014)
Scientific Reports.
, vol.4
, pp. 3678
-
-
Bhargava, V.1
Head, S.R.2
Ordoukhanian, P.3
Mercola, M.4
Subramaniam, S.5
-
21
-
-
84891677425
-
Full-length RNA-seq from single cells using Smart-seq2
-
24385147
-
Picelli S, Faridani OR, Bjorklund AK, Winberg G, Sagasser S, Sandberg R. Full-length RNA-seq from single cells using Smart-seq2. Nature protocols. 2014; 9(1):171-81. doi: 10.1038/nprot.2014.006 PMID: 24385147
-
(2014)
Nature Protocols.
, vol.9
, Issue.1
, pp. 171-181
-
-
Picelli, S.1
Faridani, O.R.2
Bjorklund, A.K.3
Winberg, G.4
Sagasser, S.5
Sandberg, R.6
-
22
-
-
84895562012
-
From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing
-
24299736 PubMed Central PMCID: PMC3941114
-
Marinov GK, Williams BA, McCue K, Schroth GP, Gertz J, Myers RM, et al. From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome research. 2014; 24 (3):496-510. PubMed Central PMCID: PMC3941114. doi: 10.1101/gr.161034.113 PMID: 24299736
-
(2014)
Genome Research.
, vol.24
, Issue.3
, pp. 496-510
-
-
Marinov, G.K.1
Williams, B.A.2
McCue, K.3
Schroth, G.P.4
Gertz, J.5
Myers, R.M.6
-
23
-
-
84887101406
-
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
-
24056875
-
Picelli S, Bjorklund AK, Faridani OR, Sagasser S, Winberg G, Sandberg R. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nature methods. 2013; 10(11):1096-8. doi: 10.1038/ nmeth.2639 PMID: 24056875
-
(2013)
Nature Methods.
, vol.10
, Issue.11
, pp. 1096-1098
-
-
Picelli, S.1
Bjorklund, A.K.2
Faridani, O.R.3
Sagasser, S.4
Winberg, G.5
Sandberg, R.6
-
24
-
-
0033559113
-
Amplification of cDNA ends based on template-switching effect and step-out PCR
-
10037822 PubMed Central PMCID: PMC148354
-
Matz M, Shagin D, Bogdanova E, Britanova O, Lukyanov S, Diatchenko L, et al. Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic acids research. 1999; 27(6):1558-60. PubMed Central PMCID: PMC148354. PMID: 10037822
-
(1999)
Nucleic Acids Research.
, vol.27
, Issue.6
, pp. 1558-1560
-
-
Matz, M.1
Shagin, D.2
Bogdanova, E.3
Britanova, O.4
Lukyanov, S.5
Diatchenko, L.6
-
25
-
-
84907569164
-
Capture and Amplification by Tailing and Switching (CATS). An ultrasensitive ligation-independent method for generation of DNA libraries for deep sequencing from picogram amounts of DNA and RNA
-
24922482 PubMed Central PMCID: PMC4179956
-
Turchinovich A, Surowy H, Serva A, Zapatka M, Lichter P, Burwinkel B. Capture and Amplification by Tailing and Switching (CATS). An ultrasensitive ligation-independent method for generation of DNA libraries for deep sequencing from picogram amounts of DNA and RNA. RNA biology. 2014; 11(7):817-28. PubMed Central PMCID: PMC4179956. doi: 10.4161/rna.29304 PMID: 24922482
-
(2014)
RNA Biology.
, vol.11
, Issue.7
, pp. 817-828
-
-
Turchinovich, A.1
Surowy, H.2
Serva, A.3
Zapatka, M.4
Lichter, P.5
Burwinkel, B.6
-
26
-
-
84873664803
-
Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching
-
23180801 PubMed Central PMCID: PMC3562004
-
Tang DT, Plessy C, Salimullah M, Suzuki AM, Calligaris R, Gustincich S, et al. Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching. Nucleic acids research. 2013; 41(3):e44. PubMed Central PMCID: PMC3562004. doi: 10.1093/nar/gks1128 PMID: 23180801
-
(2013)
Nucleic Acids Research.
, vol.41
, Issue.3
, pp. e44
-
-
Tang, D.T.1
Plessy, C.2
Salimullah, M.3
Suzuki, A.M.4
Calligaris, R.5
Gustincich, S.6
-
27
-
-
0021764894
-
Long poly(A) tracts in the human genome are associated with the Alu family of repeated elements
-
6241262
-
Lustig AJ, Petes TD. Long poly(A) tracts in the human genome are associated with the Alu family of repeated elements. Journal of molecular biology. 1984; 180(3):753-9. PMID: 6241262
-
(1984)
Journal of Molecular Biology.
, vol.180
, Issue.3
, pp. 753-759
-
-
Lustig, A.J.1
Petes, T.D.2
-
28
-
-
77949569085
-
Terminal deoxynucleotidyl transferase: The story of a misguided DNA polymerase
-
19596089 PubMed Central PMCID: PMC2846215
-
Motea EA, Berdis AJ. Terminal deoxynucleotidyl transferase: the story of a misguided DNA polymerase. Biochimica et biophysica acta. 2010; 1804(5):1151-66. PubMed Central PMCID: PMC2846215. doi: 10.1016/j.bbapap.2009.06.030 PMID: 19596089
-
(2010)
Biochimica et Biophysica Acta.
, vol.1804
, Issue.5
, pp. 1151-1166
-
-
Motea, E.A.1
Berdis, A.J.2
-
29
-
-
78651437467
-
NanoCAGE: A high-resolution technique to discover and interrogate cell transcriptomes
-
21205859 PubMed Central PMCID: PMC4181851 pdb prot5559
-
Salimullah M, Sakai M, Plessy C, Carninci P. NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes. Cold Spring Harbor protocols. 2011; 2011(1):pdb prot5559. PubMed Central PMCID: PMC4181851. doi: 10.1101/pdb.prot5559 PMID: 21205859
-
(2011)
Cold Spring Harbor Protocols.
, vol.2011
, Issue.1
-
-
Salimullah, M.1
Sakai, M.2
Plessy, C.3
Carninci, P.4
-
30
-
-
84949221539
-
Mapping replication origin sequences in eukaryotic chromosomes
-
/ editorial board, Bonifacino Juan S [et al]. PubMed Central PMCID: PMC4274620.
-
Fu H, Besnard E, Desprat R, Ryan M, Kahli M, Lemaitre JM, et al. Mapping replication origin sequences in eukaryotic chromosomes. Current protocols in cell biology / editorial board, Bonifacino Juan S [et al]. 2014; 65:2201-017. PubMed Central PMCID: PMC4274620.
-
(2014)
Current Protocols in Cell Biology
, vol.65
, pp. 2201-3017
-
-
Fu, H.1
Besnard, E.2
Desprat, R.3
Ryan, M.4
Kahli, M.5
Lemaitre, J.M.6
-
31
-
-
84866303839
-
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals
-
22940246 PubMed Central PMCID: PMC3873101
-
Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Molecular cell. 2012; 47(5):810-22. PubMed Central PMCID: PMC3873101. doi: 10.1016/j.molcel.2012.07.030 PMID: 22940246
-
(2012)
Molecular Cell.
, vol.47
, Issue.5
, pp. 810-822
-
-
Garber, M.1
Yosef, N.2
Goren, A.3
Raychowdhury, R.4
Thielke, A.5
Guttman, M.6
-
32
-
-
84907419194
-
Immunogenetics.Chromatin state dynamics during blood formation
-
25103404 PubMed Central PMCID: PMC4412442
-
Lara-Astiaso D, Weiner A, Lorenzo-Vivas E, Zaretsky I, Jaitin DA, David E, et al. Immunogenetics. Chromatin state dynamics during blood formation. Science. 2014; 345(6199):943-9. PubMed Central PMCID: PMC4412442. doi: 10.1126/science.1256271 PMID: 25103404
-
(2014)
Science
, vol.345
, Issue.6199
, pp. 943-949
-
-
Lara-Astiaso, D.1
Weiner, A.2
Lorenzo-Vivas, E.3
Zaretsky, I.4
Jaitin, D.A.5
David, E.6
-
33
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
22388286 PubMed Central PMCID: PMC3322381
-
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature methods. 2012; 9 (4):357-9. PubMed Central PMCID: PMC3322381. doi: 10.1038/nmeth.1923 PMID: 22388286
-
(2012)
Nature Methods.
, vol.9
, Issue.4
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
34
-
-
0034201441
-
EMBOSS: The european molecular biology open software suite
-
10827456
-
Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends in genetics: TIG. 2000; 16(6):276-7. PMID: 10827456
-
(2000)
Trends in Genetics: TIG.
, vol.16
, Issue.6
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
35
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
20110278 PubMed Central PMCID: PMC2832824
-
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6):841-2. PubMed Central PMCID: PMC2832824. doi: 10.1093/bioinformatics/btq033 PMID: 20110278
-
(2010)
Bioinformatics.
, vol.26
, Issue.6
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
36
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
19505943 PubMed Central PMCID: PMC2723002
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PubMed Central PMCID: PMC2723002. doi: 10.1093/bioinformatics/btp352 PMID: 19505943
-
(2009)
Bioinformatics.
, vol.25
, Issue.16
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
-
37
-
-
2142738304
-
WebLogo: A sequence logo generator
-
15173120 PubMed Central PMCID: PMC419797
-
Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome research. 2004; 14(6):1188-90. PubMed Central PMCID: PMC419797. doi: 10.1101/gr.849004 PMID: 15173120
-
(2004)
Genome Research.
, vol.14
, Issue.6
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
38
-
-
84866442229
-
On effect size
-
22545595
-
Kelley K, Preacher KJ. On effect size. Psychological methods. 2012; 17(2):137-52. doi: 10.1037/ a0028086 PMID: 22545595
-
(2012)
Psychological Methods.
, vol.17
, Issue.2
, pp. 137-152
-
-
Kelley, K.1
Preacher, K.J.2
|