-
1
-
-
52449114817
-
Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities
-
Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I: Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 2008, 3(8):e3042.
-
(2008)
PLoS One
, vol.3
, Issue.8
-
-
Gilbert, J.A.1
Field, D.2
Huang, Y.3
Edwards, R.4
Li, W.5
Gilna, P.6
Joint, I.7
-
2
-
-
41649114407
-
Microbial community gene expression in ocean surface waters
-
Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, Delong EF: Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A 2008, 105(10):3805-3810.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, Issue.10
, pp. 3805-3810
-
-
Frias-Lopez, J.1
Shi, Y.2
Tyson, G.W.3
Coleman, M.L.4
Schuster, S.C.5
Chisholm, S.W.6
Delong, E.F.7
-
3
-
-
66649089244
-
Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre
-
Poretsky RS, Hewson I, Sun S, Allen AE, Zehr JP, Moran MA: Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environ Microbiol 2009, 11(6):1358-1375.
-
(2009)
Environ Microbiol
, vol.11
, Issue.6
, pp. 1358-1375
-
-
Poretsky, R.S.1
Hewson, I.2
Sun, S.3
Allen, A.E.4
Zehr, J.P.5
Moran, M.A.6
-
4
-
-
67349276620
-
In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii
-
Hewson I, Poretsky RS, Beinart RA, White AE, Shi T, Bench SR, Moisander PH, Paerl RW, Tripp HJ, Montoya JP, Moran MA, Zehr JP: In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii. ISME J 2009, 3(5):618-631.
-
(2009)
ISME J
, vol.3
, Issue.5
, pp. 618-631
-
-
Hewson, I.1
Poretsky, R.S.2
Beinart, R.A.3
White, A.E.4
Shi, T.5
Bench, S.R.6
Moisander, P.H.7
Paerl, R.W.8
Tripp, H.J.9
Montoya, J.P.10
Moran, M.A.11
Zehr, J.P.12
-
5
-
-
70350284310
-
Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean
-
Hewson I, Poretsky RS, Dyhrman ST, Zielinski B, White AE, Tripp HJ, Montoya JP, Zehr JP: Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean. ISME J 2009, 3(11):1286-1300.
-
(2009)
ISME J
, vol.3
, Issue.11
, pp. 1286-1300
-
-
Hewson, I.1
Poretsky, R.S.2
Dyhrman, S.T.3
Zielinski, B.4
White, A.E.5
Tripp, H.J.6
Montoya, J.P.7
Zehr, J.P.8
-
6
-
-
79951810312
-
Quantitative analysis of a deeply sequenced marine microbial metatranscriptome
-
Gifford SM, Sharma S, Rinta-Kanto JM, Moran MA: Quantitative analysis of a deeply sequenced marine microbial metatranscriptome. ISME J 2011, 5(3):461-472.
-
(2011)
ISME J
, vol.5
, Issue.3
, pp. 461-472
-
-
Gifford, S.M.1
Sharma, S.2
Rinta-Kanto, J.M.3
Moran, M.A.4
-
7
-
-
84872981638
-
Expression patterns reveal niche diversification in a marine microbial assemblage
-
Gifford SM, Sharma S, Booth M, Moran MA: Expression patterns reveal niche diversification in a marine microbial assemblage. ISME J 2013, 7(2):281-298.
-
(2013)
ISME J
, vol.7
, Issue.2
, pp. 281-298
-
-
Gifford, S.M.1
Sharma, S.2
Booth, M.3
Moran, M.A.4
-
8
-
-
33747479446
-
Archaea predominate among ammonia-oxidizing prokaryotes in soils
-
Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C: Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 2006, 442(7104):806-809.
-
(2006)
Nature
, vol.442
, Issue.7104
, pp. 806-809
-
-
Leininger, S.1
Urich, T.2
Schloter, M.3
Schwark, L.4
Qi, J.5
Nicol, G.W.6
Prosser, J.I.7
Schuster, S.C.8
Schleper, C.9
-
9
-
-
84872920243
-
Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms
-
Tveit A, Schwacke R, Svenning MM, Urich T: Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms. ISME J 2013, 7(2):299-311.
-
(2013)
ISME J
, vol.7
, Issue.2
, pp. 299-311
-
-
Tveit, A.1
Schwacke, R.2
Svenning, M.M.3
Urich, T.4
-
10
-
-
49649087440
-
Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome
-
Urich T, Lanzen A, Qi J, Huson DH, Schleper C, Schuster SC: Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One 2008, 3(6):e2527.
-
(2008)
PLoS One
, vol.3
, Issue.6
-
-
Urich, T.1
Lanzen, A.2
Qi, J.3
Huson, D.H.4
Schleper, C.5
Schuster, S.C.6
-
11
-
-
79952401369
-
Metatranscriptomic approach to analyze the functional human gut microbiota
-
Gosalbes MJ, Durban A, Pignatelli M, Abellan JJ, Jimenez-Hernandez N, Perez-Cobas AE, Latorre A, Moya A: Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One 2011, 6(3):e17447.
-
(2011)
PLoS One
, vol.6
, Issue.3
-
-
Gosalbes, M.J.1
Durban, A.2
Pignatelli, M.3
Abellan, J.J.4
Jimenez-Hernandez, N.5
Perez-Cobas, A.E.6
Latorre, A.7
Moya, A.8
-
12
-
-
84884561756
-
Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton
-
Stewart FJ: Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton. Methods Enzymol 2013, 531:187-218.
-
(2013)
Methods Enzymol
, vol.531
, pp. 187-218
-
-
Stewart, F.J.1
-
13
-
-
84884582870
-
Sample processing and cDNA preparation for microbial metatranscriptomics in complex soil communities
-
Carvalhais LC, Schenk PM: Sample processing and cDNA preparation for microbial metatranscriptomics in complex soil communities. Methods Enzymol 2013, 531:251-267.
-
(2013)
Methods Enzymol
, vol.531
, pp. 251-267
-
-
Carvalhais, L.C.1
Schenk, P.M.2
-
15
-
-
50549085547
-
Isolation and analysis of mRNA from environmental microbial communities
-
McGrath KC, Thomas-Hall SR, Cheng CT, Leo L, Alexa A, Schmidt S, Schenk PM: Isolation and analysis of mRNA from environmental microbial communities. J Microbiol Methods 2008, 75(2):172-176.
-
(2008)
J Microbiol Methods
, vol.75
, Issue.2
, pp. 172-176
-
-
McGrath, K.C.1
Thomas-Hall, S.R.2
Cheng, C.T.3
Leo, L.4
Alexa, A.5
Schmidt, S.6
Schenk, P.M.7
-
16
-
-
77954086440
-
Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics
-
Stewart FJ, Ottesen EA, DeLong EF: Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. ISME J 2010, 4(7):896-907.
-
(2010)
ISME J
, vol.4
, Issue.7
, pp. 896-907
-
-
Stewart, F.J.1
Ottesen, E.A.2
DeLong, E.F.3
-
17
-
-
80455168272
-
Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq
-
Yi H, Cho YJ, Won S, Lee JE, Jin Yu H, Kim S, Schroth GP, Luo S, Chun J: Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq. Nucleic Acids Res 2011, 39(20):e140.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.20
-
-
Yi, H.1
Cho, Y.J.2
Won, S.3
Lee, J.E.4
Jin Yu, H.5
Kim, S.6
Schroth, G.P.7
Luo, S.8
Chun, J.9
-
18
-
-
84885370853
-
An efficient rRNA removal method for RNA sequencing in GC-rich bacteria
-
Peano C, Pietrelli A, Consolandi C, Rossi E, Petiti L, Tagliabue L, De Bellis G, Landini P: An efficient rRNA removal method for RNA sequencing in GC-rich bacteria. Microb Inform Exp 2013, 3(1):1.
-
(2013)
Microb Inform Exp
, vol.3
, Issue.1
, pp. 1
-
-
Peano, C.1
Pietrelli, A.2
Consolandi, C.3
Rossi, E.4
Petiti, L.5
Tagliabue, L.6
De Bellis, G.7
Landini, P.8
-
19
-
-
77957689489
-
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics
-
He S, Wurtzel O, Singh K, Froula JL, Yilmaz S, Tringe SG, Wang Z, Chen F, Lindquist EA, Sorek R, Hugenholtz P: Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nat Methods 2010, 7(10):807-812.
-
(2010)
Nat Methods
, vol.7
, Issue.10
, pp. 807-812
-
-
He, S.1
Wurtzel, O.2
Singh, K.3
Froula, J.L.4
Yilmaz, S.5
Tringe, S.G.6
Wang, Z.7
Chen, F.8
Lindquist, E.A.9
Sorek, R.10
Hugenholtz, P.11
-
20
-
-
77956603781
-
Extraction of mRNA from soil
-
Mettel C, Kim Y, Shrestha PM, Liesack W: Extraction of mRNA from soil. Appl Environ Microbiol 2010, 76(17):5995-6000.
-
(2010)
Appl Environ Microbiol
, vol.76
, Issue.17
, pp. 5995-6000
-
-
Mettel, C.1
Kim, Y.2
Shrestha, P.M.3
Liesack, W.4
-
21
-
-
84858990515
-
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
-
Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A: Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol 2012, 13(3):R23.
-
(2012)
Genome Biol
, vol.13
, Issue.3
, pp. R23
-
-
Giannoukos, G.1
Ciulla, D.M.2
Huang, K.3
Haas, B.J.4
Izard, J.5
Levin, J.Z.6
Livny, J.7
Earl, A.M.8
Gevers, D.9
Ward, D.V.10
Nusbaum, C.11
Birren, B.W.12
Gnirke, A.13
-
22
-
-
84879692466
-
Comparative analysis of RNA sequencing methods for degraded or low-input samples
-
Adiconis X, Borges-Rivera D, Satija R, Deluca DS, Busby MA, Berlin AM, Sivachenko A, Thompson DA, Wysoker A, Fennell T, Gnirke A, Pochet N, Regev A, Levin JZ: Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nat Methods 2013, 10(7):623-629.
-
(2013)
Nat Methods
, vol.10
, Issue.7
, pp. 623-629
-
-
Adiconis, X.1
Borges-Rivera, D.2
Satija, R.3
Deluca, D.S.4
Busby, M.A.5
Berlin, A.M.6
Sivachenko, A.7
Thompson, D.A.8
Wysoker, A.9
Fennell, T.10
Gnirke, A.11
Pochet, N.12
Regev, A.13
Levin, J.Z.14
-
23
-
-
77956340995
-
Comprehensive comparative analysis of strand-specific RNA sequencing methods
-
Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A: Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 2010, 7(9):709-715.
-
(2010)
Nat Methods
, vol.7
, Issue.9
, pp. 709-715
-
-
Levin, J.Z.1
Yassour, M.2
Adiconis, X.3
Nusbaum, C.4
Thompson, D.A.5
Friedman, N.6
Gnirke, A.7
Regev, A.8
-
24
-
-
84897927641
-
Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol
-
Sun Z, Asmann YW, Nair A, Zhang Y, Wang L, Kalari KR, Bhagwate AV, Baker TR, Carr JM, Kocher JP, Perez EA, Thompson EA: Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol. PLoS One 2013, 8(8):e71745.
-
(2013)
PLoS One
, vol.8
, Issue.8
-
-
Sun, Z.1
Asmann, Y.W.2
Nair, A.3
Zhang, Y.4
Wang, L.5
Kalari, K.R.6
Bhagwate, A.V.7
Baker, T.R.8
Carr, J.M.9
Kocher, J.P.10
Perez, E.A.11
Thompson, E.A.12
-
25
-
-
84867398590
-
Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification
-
Malboeuf CM, Yang X, Charlebois P, Qu J, Berlin AM, Casali M, Pesko KN, Boutwell CL, DeVincenzo JP, Ebel GD, Allen TM, Zody MC, Henn MR, Levin JZ: Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification. Nucleic Acids Res 2013, 41(1):e13.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.1
-
-
Malboeuf, C.M.1
Yang, X.2
Charlebois, P.3
Qu, J.4
Berlin, A.M.5
Casali, M.6
Pesko, K.N.7
Boutwell, C.L.8
DeVincenzo, J.P.9
Ebel, G.D.10
Allen, T.M.11
Zody, M.C.12
Henn, M.R.13
Levin, J.Z.14
-
26
-
-
84864880991
-
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
-
Ramskold D, Luo S, Wang YC, Li R, Deng Q, Faridani OR, Daniels GA, Khrebtukova I, Loring JF, Laurent LC, Schroth GP, Sandberg R: Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol 2012, 30(8):777-782.
-
(2012)
Nat Biotechnol
, 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
Daniels, G.A.7
Khrebtukova, I.8
Loring, J.F.9
Laurent, L.C.10
Schroth, G.P.11
Sandberg, R.12
-
27
-
-
84892179132
-
Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells
-
Deng Q, Ramskold D, Reinius B, Sandberg R: Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 2014, 343(6167):193-196.
-
(2014)
Science
, vol.343
, Issue.6167
, pp. 193-196
-
-
Deng, Q.1
Ramskold, D.2
Reinius, B.3
Sandberg, R.4
-
28
-
-
84872965253
-
Sizing up metatranscriptomics
-
Moran MA, Satinsky B, Gifford SM, Luo H, Rivers A, Chan LK, Meng J, Durham BP, Shen C, Varaljay VA, Smith CB, Yager PL, Hopkinson BM: Sizing up metatranscriptomics. ISME J 2013, 7(2):237-243.
-
(2013)
ISME J
, vol.7
, Issue.2
, pp. 237-243
-
-
Moran, M.A.1
Satinsky, B.2
Gifford, S.M.3
Luo, H.4
Rivers, A.5
Chan, L.K.6
Meng, J.7
Durham, B.P.8
Shen, C.9
Varaljay, V.A.10
Smith, C.B.11
Yager, P.L.12
Hopkinson, B.M.13
-
29
-
-
84988894938
-
-
FASTX-Toolkit. [http://hannonlab.cshl.edu/fastx_toolkit/index.html].
-
-
-
-
30
-
-
84870814915
-
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
-
Kopylova E, Noe L, Touzet H: SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 2012, 28(24):3211-3217.
-
(2012)
Bioinformatics
, vol.28
, Issue.24
, pp. 3211-3217
-
-
Kopylova, E.1
Noe, L.2
Touzet, H.3
-
31
-
-
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(14):1754-1760.
-
(2009)
Bioinformatics
, vol.25
, Issue.14
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
32
-
-
84876580700
-
MicroScope-an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data
-
Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S, Lajus A, Le Fevre F, Longin C, Mornico D, Roche D, Rouy Z, Salvignol G, Scarpelli C, Thil Smith AA, Weiman M, Medigue C: MicroScope-an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res 2013, 41(Database issue):D636-D647.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.DATABASE ISSUE
, pp. D636-D647
-
-
Vallenet, D.1
Belda, E.2
Calteau, A.3
Cruveiller, S.4
Engelen, S.5
Lajus, A.6
Le Fevre, F.7
Longin, C.8
Mornico, D.9
Roche, D.10
Rouy, Z.11
Salvignol, G.12
Scarpelli, C.13
Thil Smith, A.A.14
Weiman, M.15
Medigue, C.16
-
34
-
-
84988859320
-
-
Picard. In [http://broadinstitute.github.io/picard].
-
-
-
-
35
-
-
84988831699
-
-
The R Project for Statistical Computing. In [http://www.r-project.org/].
-
-
-
-
36
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biol 2010, 11(10):R106.
-
(2010)
Genome Biol
, vol.11
, Issue.10
, pp. R106
-
-
Anders, S.1
Huber, W.2
-
37
-
-
74049148179
-
3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer
-
Asmann YW, Klee EW, Thompson EA, Perez EA, Middha S, Oberg AL, Therneau TM, Smith DI, Poland GA, Wieben ED, Kocher JP: 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer. BMC Genomics 2009, 10:531.
-
(2009)
BMC Genomics
, vol.10
, pp. 531
-
-
Asmann, Y.W.1
Klee, E.W.2
Thompson, E.A.3
Perez, E.A.4
Middha, S.5
Oberg, A.L.6
Therneau, T.M.7
Smith, D.I.8
Poland, G.A.9
Wieben, E.D.10
Kocher, J.P.11
|