-
1
-
-
80053651587
-
-
Benson, D.A., Cavanaugh, M., Clark, K., Karsch-Mizrahi, I., Lipman, D.J., Ostell, J. and Sayers, E.W. (2013) GenBank, Nucleic Acids Res., 41, D36-D42.
-
(2013)
GenBank, Nucleic Acids Res.
, vol.41
, pp. D36-D42
-
-
Benson, D.A.1
Cavanaugh, M.2
Clark, K.3
Karsch-Mizrahi, I.4
Lipman, D.J.5
Ostell, J.6
Sayers, E.W.7
-
2
-
-
84976871272
-
Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation
-
O'Leary, N.A., Wright, M.W., Brister, J.R. et al. (2016) Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res., 44, D733-D745.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D733-D745
-
-
O'Leary, N.A.1
Wright, M.W.2
Brister, J.R.3
-
3
-
-
84946041374
-
The genomes online database (GOLD) v.5: A metadata management system based on a four level (meta)genome project classification
-
Reddy, T.B.K., Thomas, A., Stamatis, D., Bertsch, J., Isbandi, M., Jansson, J., Mallajosyula, J., Pagani, I., Lobos, E. and Kyrpides, N.C. (2014) The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res., 43, D1099-D1106.
-
(2014)
Nucleic Acids Res.
, vol.43
, pp. D1099-D1106
-
-
Reddy, T.B.K.1
Thomas, A.2
Stamatis, D.3
Bertsch, J.4
Isbandi, M.5
Jansson, J.6
Mallajosyula, J.7
Pagani, I.8
Lobos, E.9
Kyrpides, N.C.10
-
4
-
-
84945949405
-
The standard operating procedure of the DOE-JGI microbial genome annotation pipeline (MGAP v.4
-
Huntemann, M., Ivanova, N.N., Mavromatis, K., Tripp, H.J., Paez-Espino, D., Palaniappan, K., Szeto, E., Pillay, M., Chen, I.A., Pati, A. et al. (2015) The standard operating procedure of the DOE-JGI microbial genome annotation pipeline (MGAP v. 4). Stand. Genomic Sci., 10, 86.
-
(2015)
Stand. Genomic Sci.
, pp. 10-86
-
-
Huntemann, M.1
Ivanova, N.N.2
Mavromatis, K.3
Tripp, H.J.4
Paez-Espino, D.5
Palaniappan, K.6
Szeto, E.7
Pillay, M.8
Chen, I.A.9
Pati, A.10
-
5
-
-
34447644810
-
CRISPR Recognition Tool (CRT): A tool for automatic detection of clustered regularly interspaced palindromic repeats
-
Bland, C., Ramsey, T.L., Sabree, F., Lowe, M., Brown, K., Kyrpides, N.C. and Hugenholtz, P. (2007) CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics, 8, 209.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 209
-
-
Bland, C.1
Ramsey, T.L.2
Sabree, F.3
Lowe, M.4
Brown, K.5
Kyrpides, N.C.6
Hugenholtz, P.7
-
6
-
-
84890037468
-
Infernal 1.1: 100-fold faster RNA homology searches
-
Nawrocki, E.P. and Eddy, S.R. (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics, 29, 2933-2935.
-
(2013)
Bioinformatics
, vol.29
, pp. 2933-2935
-
-
Nawrocki, E.P.1
Eddy, S.R.2
-
7
-
-
13444252847
-
Rfam: Annotating non-coding RNAs in complete genomes
-
Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R. and Bateman, A. (2015) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res., 33, D121-D124.
-
(2015)
Nucleic Acids Res.
, vol.33
, pp. D121-D124
-
-
Griffiths-Jones, S.1
Moxon, S.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
Bateman, A.6
-
8
-
-
65549111754
-
Infernal 1.0: Inference of RNA alignments
-
Nawrocki, E.P., Kolbe, D.L. and Eddy, S.R. (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337.
-
(2009)
Bioinformatics
, vol.25
, pp. 1335-1337
-
-
Nawrocki, E.P.1
Kolbe, D.L.2
Eddy, S.R.3
-
9
-
-
77952299957
-
Prodigal: Prokaryotic gene recognition and translation initiation site identification
-
Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, FW and Hauser, L.J. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11, 119.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 119
-
-
Hyatt, D.1
Chen, G.L.2
Locascio, P.F.3
Land, M.L.4
Larimer, F.W.5
Hauser, L.J.6
-
10
-
-
34248531753
-
Locating proteins in the cell using TargetP, SignalP, and related tools
-
Emanuelsson, O., Brunak, S., von Heijne, G. and Nielsen, H. (2007) Locating proteins in the cell using TargetP, SignalP, and related tools. Nat. Protoc., 2, 953-971.
-
(2007)
Nat. Protoc.
, vol.2
, pp. 953-971
-
-
Emanuelsson, O.1
Brunak, S.2
Von Heijne, G.3
Nielsen, H.4
-
11
-
-
0034899781
-
Evaluation of methods for the prediction of membrane spanning regions
-
Moller, S., Croning, M.D.R. and Apweiler, R. (2001) Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics, 17, 646-653.
-
(2001)
Bioinformatics
, vol.17
, pp. 646-653
-
-
Moller, S.1
Croning, M.D.R.2
Apweiler, R.3
-
12
-
-
84941067064
-
Expanded microbial genome coverage and improved protein family annotation in the COG database
-
Galperin, M.Y., Makarova, K.S., Wolf, Y.I. and Koonin, E.V. (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res., 43, D261-D269.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D261-D269
-
-
Galperin, M.Y.1
Makarova, K.S.2
Wolf, Y.I.3
Koonin, E.V.4
-
13
-
-
84976865403
-
The Pfam protein families database: Towards a more sustainable future
-
Finn, R.D., Coggill, P., Eberhardt, R.Y. et al. (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res., 44, D279-D285.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D279-D285
-
-
Finn, R.D.1
Coggill, P.2
Eberhardt, R.Y.3
-
14
-
-
84876134492
-
TIGRFAMs and genome properties in 2013
-
Haft, D.H., Selengut, J.D., Richter, R.A., Harkins, D., Basu, M.K. and Beck, E. (2013) TIGRFAMs and genome properties in 2013. Nucleic Acids Res., 41, D387-D395.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D387-D395
-
-
Haft, D.H.1
Selengut, J.D.2
Richter, R.A.3
Harkins, D.4
Basu, M.K.5
Beck, E.6
-
15
-
-
84941349095
-
HMMER web server: 2015 update
-
Finn, R.D., Clements, J., Arndt, W. et al. (2015) HMMER web server: 2015 update. Nucleic Acids Res., 43, W30-W38.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. W30-W38
-
-
Finn, R.D.1
Clements, J.2
Arndt, W.3
-
16
-
-
84899518211
-
InterProScan 5: Genome-scale protein function classification
-
Jones, P., Binns, D., Chang, H-Y et al. (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics., 30, 1236-1240.
-
(2014)
Bioinformatics.
, vol.30
, pp. 1236-1240
-
-
Jones, P.1
Binns, D.2
Chang, H.-Y.3
-
17
-
-
84976907502
-
KEGG as a reference resource for gene and protein annotation
-
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M. (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res., 44, D457-D462.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D457-D462
-
-
Kanehisa, M.1
Sato, Y.2
Kawashima, M.3
Furumichi, M.4
Tanabe, M.5
-
18
-
-
79952256999
-
Adaptive seeds tame genomic sequence comparison
-
Kielbasa, S.M., Wan, R., Sato, K., Horton, P. and Frith, M.C. (2011) Adaptive seeds tame genomic sequence comparison. Genome Res., 21, 487-493.
-
(2011)
Genome Res.
, vol.21
, pp. 487-493
-
-
Kielbasa, S.M.1
Wan, R.2
Sato, K.3
Horton, P.4
Frith, M.C.5
-
19
-
-
84976877782
-
TheMetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
-
Caspi, R., Billington, R., Ferrer, L. et al. (2016) TheMetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 44, D471-D480.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D471-D480
-
-
Caspi, R.1
Billington, R.2
Ferrer, L.3
-
20
-
-
38549166674
-
Metabolic reconstruction of microbial genomes and microbial community metagenomes
-
Lawrence Berkeley National Laboratory
-
Ivanova, N.N., Anderson, I., Lykidis, A., Mavrommatis, K., Mikhailova, N., Chen, I.A., Szeto, E., Palaniappan, K., Markowitz, V.M. and Kyrpides, N.C. (2007) Metabolic Reconstruction of Microbial Genomes and Microbial Community Metagenomes. Technical Report 62292, Lawrence Berkeley National Laboratory.
-
(2007)
Technical Report 62292
-
-
Ivanova, N.N.1
Anderson, I.2
Lykidis, A.3
Mavrommatis, K.4
Mikhailova, N.5
Chen, I.A.6
Szeto, E.7
Palaniappan, K.8
Markowitz, V.M.9
Kyrpides, N.C.10
-
21
-
-
84873739550
-
Improving microbial genome annotations in an integrated database context
-
Chen, I.A., Markowitz, V.M., Chu, K., Anderson, I., Mavromatis, K., Kyrpides, N.C. and Ivanova, N.N. (2013) Improving microbial genome annotations in an integrated database context, PLoS ONE, 8, e54859.
-
(2013)
PLoS ONE
, vol.8
, pp. e54859
-
-
Chen, I.A.1
Markowitz, V.M.2
Chu, K.3
Anderson, I.4
Mavromatis, K.5
Kyrpides, N.C.6
Ivanova, N.N.7
-
22
-
-
84946034354
-
Microbial species delineation using whole genome sequences
-
Varghese, N.J., Mukherjee, S., Ivanova, N., Konstantinidis, K.T., Mavrommatis, K., Kyrpides, N.C. and Pati, A. (2015) Microbial species delineation using whole genome sequences. Nucleic Acids Res., 43, 6761-6771.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 6761-6771
-
-
Varghese, N.J.1
Mukherjee, S.2
Ivanova, N.3
Konstantinidis, K.T.4
Mavrommatis, K.5
Kyrpides, N.C.6
Pati, A.7
-
23
-
-
71049180352
-
Gene context analysis in the integrated microbial genomes (IMG) data management system, accepted for publication
-
Mavromatis, K., Chu, K., Ivanova, N., Hooper, S.D., Markowitz, V.M. and Kyrpides, N.C. (2009) Gene context analysis in the Integrated Microbial Genomes (IMG) data management system, accepted for publication, PLoS ONE, 4, e7979.
-
(2009)
PLoS ONE
, vol.4
, pp. e7979
-
-
Mavromatis, K.1
Chu, K.2
Ivanova, N.3
Hooper, S.D.4
Markowitz, V.M.5
Kyrpides, N.C.6
-
24
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
Enright, A.J., Iliopoulos, I., Kyrpides, N.C. and Ouzounis, C.A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature, 402, 86-90.
-
(1999)
Nature
, vol.402
, pp. 86-90
-
-
Enright, A.J.1
Iliopoulos, I.2
Kyrpides, N.C.3
Ouzounis, C.A.4
-
25
-
-
84939493603
-
IMG-ABC: A knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites
-
Hadjithomas, M., Chen, I.A., Chu, K., Ratner, A., Palaniappan, K., Szeto, E., Huang, J., Reddy, T.B.K., Cimermančič, P., Fischbach, M.A. et al. (2015) IMG-ABC: a knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites. mBio, 6, doi:10.1128/mBio.00932-15.
-
(2015)
MBio
, vol.6
-
-
Hadjithomas, M.1
Chen, I.A.2
Chu, K.3
Ratner, A.4
Palaniappan, K.5
Szeto, E.6
Huang, J.7
Reddy, T.B.K.8
Cimermančič, P.9
Fischbach, M.A.10
-
26
-
-
84971330173
-
The standard operating procedure of the DOE-JGI metagenome annotation pipeline (MAP v. 4)
-
Huntemann, M., Ivanova, N.N., Mavromatis, K., Tripp, H.J., Paez-Espino, D., Tennessen, K., Palaniappan, K., Szeto, E., Pillay, M., Chen, I.A. et al. (2015) The standard operating procedure of the DOE-JGI metagenome annotation pipeline (MAP v. 4). Stand. Genomic Sci., 11, 17.
-
(2015)
Stand. Genomic Sci.
, vol.11
, pp. 17
-
-
Huntemann, M.1
Ivanova, N.N.2
Mavromatis, K.3
Tripp, H.J.4
Paez-Espino, D.5
Tennessen, K.6
Palaniappan, K.7
Szeto, E.8
Pillay, M.9
Chen, I.A.10
-
27
-
-
84891820094
-
IMG 4 version of the integrated microbial genomes comparative analysis system
-
Markowitz, V.M., Chen, I.A., Palaniappan, K., Chu, K., Szeto, E., Pillay, M., Ratner, A., Huang, J., Woyke, T., Huntemann, M. et al. (2013) IMG 4 version of the integrated microbial genomes comparative analysis system, Nucleic Acids Res., 42, D560-D567.
-
(2013)
Nucleic Acids Res.
, vol.42
, pp. D560-D567
-
-
Markowitz, V.M.1
Chen, I.A.2
Palaniappan, K.3
Chu, K.4
Szeto, E.5
Pillay, M.6
Ratner, A.7
Huang, J.8
Woyke, T.9
Huntemann, M.10
-
28
-
-
84861898310
-
IMG: The integrated microbial genomes database and comparative analysis system
-
Markowitz, V.M., Chen, I.A., Palaniappan, K., Chu, K., Szeto, E., Grechkin, Y., Ratner, A., Biju, J., Huang, J., Williams, P. et al. (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res., 40, D115-D122.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D115-D122
-
-
Markowitz, V.M.1
Chen, I.A.2
Palaniappan, K.3
Chu, K.4
Szeto, E.5
Grechkin, Y.6
Ratner, A.7
Biju, J.8
Huang, J.9
Williams, P.10
-
29
-
-
84882974883
-
Accelerating gene context analysis using bitmaps
-
Romosan, A., Shoshani, A., Wu, K., Markowitz, V.M. and Mavromatis, K. (2013) Accelerating gene context analysis using bitmaps. Proc. of the 25th Int. Conference on Scientific and Statistical Database Management (SSDBM 2013).
-
(2013)
Proc. of the 25th Int. Conference on Scientific and Statistical Database Management (SSDBM 2013)
-
-
Romosan, A.1
Shoshani, A.2
Wu, K.3
Markowitz, V.M.4
Mavromatis, K.5
-
30
-
-
69949116874
-
IMG ER: A system for microbial annotation expert review and curation
-
Markowitz, V.M., Mavromatis, K., Ivanova, N.N., Chen, I.A., Chu, K. and Kyrpides, N.C. (2009) IMG ER: a system for microbial annotation expert review and curation. Bioinformatics, 25, 2271-2278.
-
(2009)
Bioinformatics
, vol.25
, pp. 2271-2278
-
-
Markowitz, V.M.1
Mavromatis, K.2
Ivanova, N.N.3
Chen, I.A.4
Chu, K.5
Kyrpides, N.C.6
-
31
-
-
84964301202
-
Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system
-
Chen, I.A., Markowitz, V.M., Palaniappan, K., Szeto, E., Chu, K., Huang, J., Ratner, A., Pillay, M., Hadjithomas, M., Huntemann, M. et al. (2016) Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. BMC Genomics, 17, 307.
-
(2016)
BMC Genomics
, vol.17
, pp. 307
-
-
Chen, I.A.1
Markowitz, V.M.2
Palaniappan, K.3
Szeto, E.4
Chu, K.5
Huang, J.6
Ratner, A.7
Pillay, M.8
Hadjithomas, M.9
Huntemann, M.10
-
32
-
-
84976668743
-
Algorithm 457: Finding all cliques of an undirected graph
-
Bron, C. and Kerbosch, J. (1973) Algorithm 457: finding all cliques of an undirected graph. Commun. ACM, 16, 575-577.
-
(1973)
Commun. ACM
, vol.16
, pp. 575-577
-
-
Bron, C.1
Kerbosch, J.2
-
33
-
-
84891800783
-
IMG 4 version of the integrated metagenomes comparative analysis system
-
Markowitz, V.M., Chen, I.A., Chu, K., Szeto, E., Palaniappan, k, Pillay, M., Ratner, A., Huang, J., Pagani, I., Tringe, S. et al. (2013) IMG 4 version of the integrated metagenomes comparative analysis system, Nucleic Acids Res., 42, D568-D573.
-
(2013)
Nucleic Acids Res.
, vol.42
, pp. D568-D573
-
-
Markowitz, V.M.1
Chen, I.A.2
Chu, K.3
Szeto, E.4
Palaniappan, K.5
Pillay, M.6
Ratner, A.7
Huang, J.8
Pagani, I.9
Tringe, S.10
-
34
-
-
84863628126
-
IMG/M-HMP: A metagenome comparative analysis system for the human microbiome project
-
Markowitz, V.M., Chen, I.M., Chu, K., Szeto, E., Palaniappan, K., Jacob, B., Ratner, A., Liolios, K., Pagani, I., Hunteman, M. et al. (2012) IMG/M-HMP: a metagenome comparative analysis system for the human microbiome project. PLoS ONE, 7, e40151.
-
(2012)
PLoS ONE
, vol.7
, pp. e40151
-
-
Markowitz, V.M.1
Chen, I.M.2
Chu, K.3
Szeto, E.4
Palaniappan, K.5
Jacob, B.6
Ratner, A.7
Liolios, K.8
Pagani, I.9
Hunteman, M.10
-
35
-
-
84970005900
-
Microbiome Data Science: Understanding our microbial planet
-
Kyrpides, N.C., Eloe-Fadrosh, E.A. and Ivanova, N.N. (2016) Microbiome Data Science: understanding our microbial planet. Trends Microbiol., 24, 425-427.
-
(2016)
Trends Microbiol.
, vol.24
, pp. 425-427
-
-
Kyrpides, N.C.1
Eloe-Fadrosh, E.A.2
Ivanova, N.N.3
-
36
-
-
84955490190
-
Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs
-
Eloe-Fadrosh, E.A., Paez-Espino, D., Jarett, J., Dunfield, P.F., Hedlund, B.P., Grasby, S.E., Brady, A.L., Dong, H., Briggs, B.R., Li, W-J et al.2016) Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat. Commun., 7, 10476.
-
(2016)
Nat. Commun.
, vol.7
, pp. 10476
-
-
Eloe-Fadrosh, E.A.1
Paez-Espino, D.2
Jarett, J.3
Dunfield, P.F.4
Hedlund, B.P.5
Grasby, S.E.6
Brady, A.L.7
Dong, H.8
Briggs, B.R.9
Li, W.-J.10
-
37
-
-
84901241272
-
Stop codon reassignments in the wild
-
Ivanova, N., Schwientek, P., Tripp, J.J., Rinke, C., Pati, A., Huntemann, M., Visel, A., Woyke, T., Kyrpides, N.C. and Rubin, E.M. (2014) Stop codon reassignments in the wild. Science, 344, 909-913.
-
(2014)
Science
, vol.344
, pp. 909-913
-
-
Ivanova, N.1
Schwientek, P.2
Tripp, J.J.3
Rinke, C.4
Pati, A.5
Huntemann, M.6
Visel, A.7
Woyke, T.8
Kyrpides, N.C.9
Rubin, E.M.10
-
38
-
-
84978941037
-
Metagenomics uncovers gaps in amplicon-based detection of microbial diversity
-
Eloe-Fadrosh, E.A., Ivanova, N.N., Woyke, T. and Kyrpides, N.C. (2016) Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. Nat. Microbiol., 1, 15032.
-
(2016)
Nat. Microbiol.
, vol.1
, pp. 15032
-
-
Eloe-Fadrosh, E.A.1
Ivanova, N.N.2
Woyke, T.3
Kyrpides, N.C.4
-
39
-
-
84984985848
-
Uncovering earth's virome
-
Paez-Espino, D., Eloe-Fadrosh, E.A., Pavlopoulos, G., Thomas, A.D., Huntemann, M., Pati, A., Rubin, E., Ivanova, N.N. and Kyrpides, N.C. (2016) Uncovering earth's virome. Nature, 536, 425-430.
-
(2016)
Nature
, vol.536
, pp. 425-430
-
-
Paez-Espino, D.1
Eloe-Fadrosh, E.A.2
Pavlopoulos, G.3
Thomas, A.D.4
Huntemann, M.5
Pati, A.6
Rubin, E.7
Ivanova, N.N.8
Kyrpides, N.C.9
-
40
-
-
85016095464
-
Maintaining a microbial genome & metagenome data analysis system in an academic setting
-
14, July 2014
-
Chen, I.A., Markowitz, V., Szeto, E., Palaniappan, K. and Chu, K (2014) Maintaining a microbial genome & metagenome data analysis system in an academic setting, SSDBM, 14, July 2014.
-
(2014)
SSDBM
-
-
Chen, I.A.1
Markowitz, V.2
Szeto, E.3
Palaniappan, K.4
Chu, K.5
|