-
1
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
10.1126/science.1181369, 2858594, 19815776
-
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326(5950):289-293. 10.1126/science.1181369, 2858594, 19815776.
-
(2009)
Science
, vol.326
, Issue.5950
, pp. 289-293
-
-
Lieberman-Aiden, E.1
van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
Amit, I.7
Lajoie, B.R.8
Sabo, P.J.9
Dorschner, M.O.10
Sandstrom, R.11
Bernstein, B.12
Bender, M.A.13
Groudine, M.14
Gnirke, A.15
Stamatoyannopoulos, J.16
Mirny, L.A.17
Lander, E.S.18
Dekker, J.19
-
2
-
-
84879832664
-
Generic Feature Format version 3
-
Generic Feature Format version 3. , http://www.sequenceontology.org/gff3.shtml
-
-
-
-
3
-
-
0036079158
-
The human genome browser at UCSC
-
186604, 12045153
-
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12(6):996-1006. 186604, 12045153.
-
(2002)
Genome Res
, vol.12
, Issue.6
, 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
-
4
-
-
84888279738
-
UCSC genome browser data formats
-
UCSC genome browser data formats. , http://genome.ucsc.edu/FAQ/FAQformat.html
-
-
-
-
5
-
-
84888283538
-
Definition of Gene Transfer Format
-
Definition of Gene Transfer Format. , http://mblab.wustl.edu/GTF22.html
-
-
-
-
6
-
-
77955977450
-
A standard variation file format for human genome sequences
-
10.1186/gb-2010-11-8-r88, 2945790, 20796305
-
Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K. A standard variation file format for human genome sequences. Genome Biol 2010, 11(8):R88. 10.1186/gb-2010-11-8-r88, 2945790, 20796305.
-
(2010)
Genome Biol
, vol.11
, Issue.8
-
-
Reese, M.G.1
Moore, B.2
Batchelor, C.3
Salas, F.4
Cunningham, F.5
Marth, G.T.6
Stein, L.7
Flicek, P.8
Yandell, M.9
Eilbeck, K.10
-
7
-
-
34249723701
-
The human genomic melting map
-
Liu F, Tostesen E, Sundet JK, Jenssen TK, Bock C, Jerstad GI, Thilly WG, Hovig E. The human genomic melting map. PLoS Comput Biol 2007, 3(5).
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.5
-
-
Liu, F.1
Tostesen, E.2
Sundet, J.K.3
Jenssen, T.K.4
Bock, C.5
Jerstad, G.I.6
Thilly, W.G.7
Hovig, E.8
-
8
-
-
84888279360
-
Definition of Wiggle Track Format
-
Definition of Wiggle Track Format. , http://genome.ucsc.edu/goldenPath/help/wiggle.html
-
-
-
-
9
-
-
84874659749
-
The Sequence Ontology
-
The Sequence Ontology. , http://www.sequenceontology.org
-
-
-
-
10
-
-
78650359068
-
The Genomic HyperBrowser: inferential genomics at the sequence level
-
10.1186/gb-2010-11-12-r121, 3046481, 21182759
-
Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, Liestol K, Clancy T, Ferkingstad E, Johansen M, Nygaard V, Tostesen E, Frigessi A, Hovig E. The Genomic HyperBrowser: inferential genomics at the sequence level. Genome Biol 2010, 11(12):R121. 10.1186/gb-2010-11-12-r121, 3046481, 21182759.
-
(2010)
Genome Biol
, vol.11
, Issue.12
-
-
Sandve, G.K.1
Gundersen, S.2
Rydbeck, H.3
Glad, I.K.4
Holden, L.5
Holden, M.6
Liestol, K.7
Clancy, T.8
Ferkingstad, E.9
Johansen, M.10
Nygaard, V.11
Tostesen, E.12
Frigessi, A.13
Hovig, E.14
-
11
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
10.1093/bioinformatics/btp352, 2723002, 19505943
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 10.1093/bioinformatics/btp352, 2723002, 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
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
12
-
-
2942547885
-
The distributed annotation system
-
10.1186/1471-2105-2-7, 58584, 11667947
-
Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L. The distributed annotation system. BMC Bioinformatics 2001, 2:7. 10.1186/1471-2105-2-7, 58584, 11667947.
-
(2001)
BMC Bioinformatics
, vol.2
, pp. 7
-
-
Dowell, R.D.1
Jokerst, R.M.2
Day, A.3
Eddy, S.R.4
Stein, L.5
-
13
-
-
84888282317
-
Web services provided by the Center for Biological Sequence analysis (CBS), Technical University of Denmark
-
Web services provided by the Center for Biological Sequence analysis (CBS), Technical University of Denmark. , http://www.cbs.dtu.dk/ws/
-
-
-
-
14
-
-
75849153303
-
The Universal Protein Resource (UniProt) in 2010
-
Database Issue
-
UniProt C. The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 2010, (38 Database Issue):D142-8.
-
(2010)
Nucleic Acids Res
, Issue.38
-
-
UniProt, C.1
-
15
-
-
71749098088
-
ELM: the status of the 2010 eukaryotic linear motif resource
-
Database Issue
-
Gould CM, Diella F, Via A, Puntervoll P, Gemund C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, Hughes T, Pas J, Rychlewski L, Trave G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ. ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res 2010, (38 Database Issue):D167-80.
-
(2010)
Nucleic Acids Res
, Issue.38
-
-
Gould, C.M.1
Diella, F.2
Via, A.3
Puntervoll, P.4
Gemund, C.5
Chabanis-Davidson, S.6
Michael, S.7
Sayadi, A.8
Bryne, J.C.9
Chica, C.10
Seiler, M.11
Davey, N.E.12
Haslam, N.13
Weatheritt, R.J.14
Budd, A.15
Hughes, T.16
Pas, J.17
Rychlewski, L.18
Trave, G.19
Aasland, R.20
Helmer-Citterich, M.21
Linding, R.22
Gibson, T.J.23
more..
-
16
-
-
77956509705
-
BioXSD: the common data-exchange format for everyday bioinformatics web services
-
10.1093/bioinformatics/btq391, 2935419, 20823319
-
Kalas M, Puntervoll P, Joseph A, Bartaseviciute E, Topfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, Rapacki K, Jonassen I. BioXSD: the common data-exchange format for everyday bioinformatics web services. Bioinformatics 2010, 26(18):i540-6. 10.1093/bioinformatics/btq391, 2935419, 20823319.
-
(2010)
Bioinformatics
, vol.26
, Issue.18
-
-
Kalas, M.1
Puntervoll, P.2
Joseph, A.3
Bartaseviciute, E.4
Topfer, A.5
Venkataraman, P.6
Pettifer, S.7
Bryne, J.C.8
Ison, J.9
Blanchet, C.10
Rapacki, K.11
Jonassen, I.12
-
17
-
-
79952937823
-
Efficient XML Interchange (EXI) Format 1.0
-
Efficient XML Interchange (EXI) Format 1.0. , http://www.w3.org/TR/2011/REC-exi-20110310
-
-
-
-
18
-
-
77955895425
-
BigWig and BigBed: enabling browsing of large distributed datasets
-
10.1093/bioinformatics/btq351, 2922891, 20639541
-
Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 2010, 26(17):2204-2207. 10.1093/bioinformatics/btq351, 2922891, 20639541.
-
(2010)
Bioinformatics
, vol.26
, Issue.17
, pp. 2204-2207
-
-
Kent, W.J.1
Zweig, A.S.2
Barber, G.3
Hinrichs, A.S.4
Karolchik, D.5
-
19
-
-
60849117520
-
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
-
10.1186/1471-2105-9-523, 2628906, 19061503
-
Nix DA, Courdy SJ, Boucher KM. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics 2008, 9:523. 10.1186/1471-2105-9-523, 2628906, 19061503.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 523
-
-
Nix, D.A.1
Courdy, S.J.2
Boucher, K.M.3
-
20
-
-
84888284606
-
GTrack
-
GTrack. , http://www.gtrack.no
-
-
-
-
21
-
-
84888275963
-
BioXSD example 1
-
BioXSD example 1. , http://bioxsd.org/trackExample1.xml
-
-
-
-
22
-
-
84888277795
-
BioXSD example 2
-
BioXSD example 2. , http://bioxsd.org/trackExample2.xml
-
-
-
-
23
-
-
84888284057
-
BioXSD example 3
-
BioXSD example 3. , http://bioxsd.org/trackExample3.xml
-
-
-
-
24
-
-
84888278908
-
BioXSD example 4
-
BioXSD example 4. , http://bioxsd.org/trackExample4.xml
-
-
-
-
25
-
-
84888281972
-
BioXSD example 5
-
BioXSD example 5. , http://bioxsd.org/trackExample5.xml
-
-
-
-
26
-
-
84888278132
-
Definition of BioXSD version 1.1
-
Definition of BioXSD version 1.1. , http://bioxsd.org/BioXSD-1.1.xsd
-
-
-
-
27
-
-
84888281989
-
BioXSD.org
-
BioXSD.org. , http://bioxsd.org
-
-
-
-
28
-
-
84888276010
-
The Genomic HyperBrowser
-
The Genomic HyperBrowser. , http://hyperbrowser.uio.no
-
-
-
-
29
-
-
84888278638
-
Creative Commons Attribution-NoDerivs 3.0 Unported License (CC BY-ND 3.0)
-
Creative Commons Attribution-NoDerivs 3.0 Unported License (CC BY-ND 3.0). , http://creativecommons.org/licenses/by-nd/3.0/
-
-
-
-
30
-
-
77955801615
-
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
10.1186/gb-2010-11-8-r86, 2945788, 20738864
-
Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11(8):R86. 10.1186/gb-2010-11-8-r86, 2945788, 20738864.
-
(2010)
Genome Biol
, vol.11
, Issue.8
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
31
-
-
75949108066
-
Galaxy: a web-based genome analysis tool for experimentalists
-
Unit 19.10.1
-
Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol 2010, 19:-21. Unit 19.10.1.
-
(2010)
Curr Protoc Mol Biol
, vol.19
, pp. 21
-
-
Blankenberg, D.1
Von Kuster, G.2
Coraor, N.3
Ananda, G.4
Lazarus, R.5
Mangan, M.6
Nekrutenko, A.7
Taylor, J.8
-
32
-
-
33750306080
-
-
Trelgol Trelgol Publishing
-
Oliphant T. Guide to NumPy 2006, Trelgol Trelgol Publishing.
-
(2006)
Guide to NumPy
-
-
Oliphant, T.1
-
33
-
-
84870403285
-
The Python Language Reference
-
The Python Language Reference. , http://docs.python.org/release/2.7.2/reference/index.html
-
-
-
-
34
-
-
0003829611
-
GNU General Public License, version 3
-
GNU General Public License, version 3. , http://www.gnu.org/copyleft/gpl.html
-
-
-
-
35
-
-
79951993896
-
Tabix: fast retrieval of sequence features from generic TAB-delimited files
-
10.1093/bioinformatics/btq671, 3042176, 21208982
-
Li H. Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics 2011, 27(5):718-719. 10.1093/bioinformatics/btq671, 3042176, 21208982.
-
(2011)
Bioinformatics
, vol.27
, Issue.5
, pp. 718-719
-
-
Li, H.1
-
36
-
-
84888283836
-
Affymetrix CNT File Format
-
Affymetrix CNT File Format. , http://goldenhelix.com/SNP_Variation/Manual/svs7/affymetrix_cnt_file_format.html
-
-
-
-
37
-
-
84888276007
-
VCF (Variant Call Format) version 4.1
-
VCF (Variant Call Format) version 4.1. , http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
-
-
-
-
38
-
-
84874653244
-
The SAM Format Specification (v1.4-r985)
-
The SAM Format Specification (v1.4-r985). , http://samtools.sourceforge.net/SAM1.pdf
-
-
-
-
39
-
-
84888284197
-
BioHDF
-
BioHDF. , http://www.hdfgroup.org/projects/biohdf/
-
-
-
-
40
-
-
84888277380
-
FASTA
-
FASTA. , http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml
-
-
-
-
41
-
-
77953909503
-
The Genomedata format for storing large-scale functional genomics data
-
10.1093/bioinformatics/btq164, 2872006, 20435580
-
Hoffman MM, Buske OJ, Noble WS. The Genomedata format for storing large-scale functional genomics data. Bioinformatics 2010, 26(11):1458-1459. 10.1093/bioinformatics/btq164, 2872006, 20435580.
-
(2010)
Bioinformatics
, vol.26
, Issue.11
, pp. 1458-1459
-
-
Hoffman, M.M.1
Buske, O.J.2
Noble, W.S.3
|