-
1
-
-
7444260846
-
The ENCODE (ENCyclopedia Of DNA Elements) Project
-
10.1126/science.1105136, 15499007, The ENCODE Project Consortium
-
The ENCODE Project Consortium The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004, 306:636-640. 10.1126/science.1105136, 15499007, The ENCODE Project Consortium.
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
2
-
-
77951230100
-
Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
-
10.1093/nar/gkp1012, 2817454, 19906703
-
Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludascher B, Korf I, Farnham PJ. Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucl Acids Res 2010, 38(3):e13. 10.1093/nar/gkp1012, 2817454, 19906703.
-
(2010)
Nucl Acids Res
, vol.38
, Issue.3
-
-
Blahnik, K.R.1
Dou, L.2
O'Geen, H.3
McPhillips, T.4
Xu, X.5
Cao, A.R.6
Iyengar, S.7
Nicolet, C.M.8
Ludascher, B.9
Korf, I.10
Farnham, P.J.11
-
3
-
-
72949087527
-
Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: evolutionary footprints of RNA silencing
-
10.1039/b903031j, 19452047
-
Feng J, Naiman DQ, Cooper B. Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: evolutionary footprints of RNA silencing. Molecular BioSystems 2009, 5:1679-1687. 10.1039/b903031j, 19452047.
-
(2009)
Molecular BioSystems
, vol.5
, pp. 1679-1687
-
-
Feng, J.1
Naiman, D.Q.2
Cooper, B.3
-
4
-
-
33646242293
-
Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes
-
10.1073/pnas.0601688103, 1447521, 16636294
-
Rigoutsos I, Huynh T, Miranda K, Tsirigos A, McHardy A, Platt D. Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. Proc Natl Acad Sci U S A 2006, 103:6605-6610. 10.1073/pnas.0601688103, 1447521, 16636294.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 6605-6610
-
-
Rigoutsos, I.1
Huynh, T.2
Miranda, K.3
Tsirigos, A.4
McHardy, A.5
Platt, D.6
-
5
-
-
34547492749
-
Genomic Signatures from DNA Word Graphs
-
Springer Berlin/Heidelberg, Mandoiu I, Zelikovsky A, Lecture Notes in Computer Science, vol 4463
-
Heath L, Pati A. Genomic Signatures from DNA Word Graphs. Bioinformatics Research and Applications 2007, 317-328. Springer Berlin/Heidelberg, Mandoiu I, Zelikovsky A, Lecture Notes in Computer Science, vol 4463.
-
(2007)
Bioinformatics Research and Applications
, pp. 317-328
-
-
Heath, L.1
Pati, A.2
-
6
-
-
0012621510
-
Separating real motifs from their artifacts
-
Blanchette M, Sinha S. Separating real motifs from their artifacts. Bioinformatics 2001, 17:S30-38.
-
(2001)
Bioinformatics
, vol.17
-
-
Blanchette, M.1
Sinha, S.2
-
7
-
-
53749093398
-
Seeder: discriminative seeding DNA motif discovery
-
10.1093/bioinformatics/btn444, 2562012, 18718942
-
Fauteux F, Blanchette M, Stromvik MV. Seeder: discriminative seeding DNA motif discovery. Bioinformatics 2008, 24:2303-2307. 10.1093/bioinformatics/btn444, 2562012, 18718942.
-
(2008)
Bioinformatics
, vol.24
, pp. 2303-2307
-
-
Fauteux, F.1
Blanchette, M.2
Stromvik, M.V.3
-
8
-
-
78449245697
-
R'MES: Finding Exceptional Motifs, version 3
-
L'institut nationl de la recherché agronomique;
-
Hoebeke M, Schbath S. R'MES: Finding Exceptional Motifs, version 3. User Guide 2006, L'institut nationl de la recherché agronomique;.
-
(2006)
User Guide
-
-
Hoebeke, M.1
Schbath, S.2
-
10
-
-
80053455778
-
Spelling Approximate Repeated or Common Motifs Using a Suffix Tree
-
Springer: Berlin/Heidelberg, Lucchesi C, Moura A, Lecture Notes in Computer Science vol 1380
-
Sagot M-F. Spelling Approximate Repeated or Common Motifs Using a Suffix Tree. LATIN'98: Theoretical Informatics 1998, 374-390. Springer: Berlin/Heidelberg, Lucchesi C, Moura A, Lecture Notes in Computer Science vol 1380.
-
(1998)
LATIN'98: Theoretical Informatics
, pp. 374-390
-
-
Sagot, M.-F.1
-
11
-
-
0029365207
-
Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences
-
10.1089/cmb.1995.2.417, 8521272
-
Schbath S, Prum B, de Turckheim E. Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences. J Comput Biol 1995, 2:417-437. 10.1089/cmb.1995.2.417, 8521272.
-
(1995)
J Comput Biol
, vol.2
, pp. 417-437
-
-
Schbath, S.1
Prum, B.2
de Turckheim, E.3
-
13
-
-
0034564539
-
A statistical method for finding transcription factor binding sites
-
The AAAI Press, Menlo Park, Russ Altman, Timothy L. Bailey, Philip Bourne, Michael Gribskov, Thomas Lengauer, Ilya N. Shindyalov, Lynn F.Ten Eyck, and Helge Weissig
-
Sinha S, Tompa M. A statistical method for finding transcription factor binding sites. Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology: 19-23 August 2000; La Jolla 2000, 344-354. The AAAI Press, Menlo Park, Russ Altman, Timothy L. Bailey, Philip Bourne, Michael Gribskov, Thomas Lengauer, Ilya N. Shindyalov, Lynn F.Ten Eyck, and Helge Weissig.
-
(2000)
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology: 19-23 August 2000; La Jolla
, pp. 344-354
-
-
Sinha, S.1
Tompa, M.2
-
14
-
-
0042905768
-
YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation
-
10.1093/nar/gkg618, 169024, 12824371
-
Sinha S, Tompa M. YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucl Acids Res 2003, 31:3586-3588. 10.1093/nar/gkg618, 169024, 12824371.
-
(2003)
Nucl Acids Res
, vol.31
, pp. 3586-3588
-
-
Sinha, S.1
Tompa, M.2
-
15
-
-
23144460837
-
WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar
-
10.1093/nar/gki492, 1160252, 15980501
-
Wang G, Yu T, Zhang W. WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar. Nucl Acids Res 2005, 33:W412-416. 10.1093/nar/gki492, 1160252, 15980501.
-
(2005)
Nucl Acids Res
, vol.33
-
-
Wang, G.1
Yu, T.2
Zhang, W.3
-
16
-
-
33745631199
-
A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements
-
10.1186/gb-2006-7-6-r49, 1779545, 16787547
-
Wang G, Zhang W. A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements. Genome Biol 2006, 7:R49. 10.1186/gb-2006-7-6-r49, 1779545, 16787547.
-
(2006)
Genome Biol
, vol.7
-
-
Wang, G.1
Zhang, W.2
-
17
-
-
3242884167
-
Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes
-
10.1093/nar/gkh465, 441603, 15215380
-
Pavesi G, Mereghetti P, Mauri G, Pesole G. Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucl Acids Res 2004, 32:W199-203. 10.1093/nar/gkh465, 441603, 15215380.
-
(2004)
Nucl Acids Res
, vol.32
-
-
Pavesi, G.1
Mereghetti, P.2
Mauri, G.3
Pesole, G.4
-
18
-
-
0035890910
-
REPuter: the manifold applications of repeat analysis on a genomic scale
-
10.1093/nar/29.22.4633, 92531, 11713313
-
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucl Acids Res 2001, 29:4633-4642. 10.1093/nar/29.22.4633, 92531, 11713313.
-
(2001)
Nucl Acids Res
, vol.29
, pp. 4633-4642
-
-
Kurtz, S.1
Choudhuri, J.V.2
Ohlebusch, E.3
Schleiermacher, C.4
Stoye, J.5
Giegerich, R.6
-
19
-
-
0034100094
-
Efficient detection of unusual words
-
10.1089/10665270050081397, 10890389
-
Apostolico A, Bock ME, Lonardi S, Xu X. Efficient detection of unusual words. J Comput Biol 2000, 7:71-94. 10.1089/10665270050081397, 10890389.
-
(2000)
J Comput Biol
, vol.7
, pp. 71-94
-
-
Apostolico, A.1
Bock, M.E.2
Lonardi, S.3
Xu, X.4
-
20
-
-
0034565285
-
Combinatorial approaches to finding subtle signals in DNA sequences
-
The AAAI Press, Menlo Park, Russ Altman, Timothy L. Bailey, Philip Bourne, Michael Gribskov, Thomas Lengauer, Ilya N.Shindyalov, Lynn F.TenEyck, and Helge Weissig
-
Pevzner PA, Sze SH. Combinatorial approaches to finding subtle signals in DNA sequences. Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology: 19-23 August 2000; La Jolla 2000, 269-278. The AAAI Press, Menlo Park, Russ Altman, Timothy L. Bailey, Philip Bourne, Michael Gribskov, Thomas Lengauer, Ilya N.Shindyalov, Lynn F.TenEyck, and Helge Weissig.
-
(2000)
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology: 19-23 August 2000; La Jolla
, pp. 269-278
-
-
Pevzner, P.A.1
Sze, S.H.2
-
21
-
-
0344376570
-
Finding composite regulatory patterns in DNA sequences
-
Eskin E, Pevzner PA. Finding composite regulatory patterns in DNA sequences. Bioinformatics 2002, 18:S354-363.
-
(2002)
Bioinformatics
, vol.18
-
-
Eskin, E.1
Pevzner, P.A.2
-
22
-
-
0031684427
-
Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm
-
10.1093/bioinformatics/14.1.55, 9520502
-
Rigoutsos I, Floratos A. Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics 1998, 14:55-67. 10.1093/bioinformatics/14.1.55, 9520502.
-
(1998)
Bioinformatics
, vol.14
, pp. 55-67
-
-
Rigoutsos, I.1
Floratos, A.2
-
23
-
-
0003037529
-
Reducibility Among Combinatorial Problems
-
New York: Plenum, Miller RE, Thatcher JW
-
Karp RM. Reducibility Among Combinatorial Problems. Complexity of Computer Computations 1972, 85-103. New York: Plenum, Miller RE, Thatcher JW.
-
(1972)
Complexity of Computer Computations
, pp. 85-103
-
-
Karp, R.M.1
-
24
-
-
0006921491
-
On the Time Complexity of the TEIRESIAS Algorithm
-
IBM T.J. Watson Research Center
-
Floratos A, Rigoutsos I. On the Time Complexity of the TEIRESIAS Algorithm. Research Report 1998, IBM T.J. Watson Research Center.
-
(1998)
Research Report
-
-
Floratos, A.1
Rigoutsos, I.2
-
25
-
-
67650556404
-
Word-based characterization of promoters involved in human DNA repair pathways
-
10.1186/1471-2164-10-S1-S18, 2709261, 19594877
-
Lichtenberg J, Jacox E, Welch J, Kurz K, Liang X, Yang M, Drews F, Ecker K, Lee S, Elnitski L, Welch L. Word-based characterization of promoters involved in human DNA repair pathways. BMC Genomics 2009, 10(Suppl 1):S18. 10.1186/1471-2164-10-S1-S18, 2709261, 19594877.
-
(2009)
BMC Genomics
, vol.10
, Issue.SUPPL 1
-
-
Lichtenberg, J.1
Jacox, E.2
Welch, J.3
Kurz, K.4
Liang, X.5
Yang, M.6
Drews, F.7
Ecker, K.8
Lee, S.9
Elnitski, L.10
Welch, L.11
-
26
-
-
70449713663
-
The word landscape of the non-coding segments of the Arabidopsis thaliana genome
-
10.1186/1471-2164-10-463, 2770528, 19814816
-
Lichtenberg J, Yilmaz A, Welch J, Kurz K, Liang X, Drews F, Ecker K, Lee S, Geisler M, Grotewold E, Welch L. The word landscape of the non-coding segments of the Arabidopsis thaliana genome. BMC Genomics 2009, 10:463. 10.1186/1471-2164-10-463, 2770528, 19814816.
-
(2009)
BMC Genomics
, vol.10
, pp. 463
-
-
Lichtenberg, J.1
Yilmaz, A.2
Welch, J.3
Kurz, K.4
Liang, X.5
Drews, F.6
Ecker, K.7
Lee, S.8
Geisler, M.9
Grotewold, E.10
Welch, L.11
-
27
-
-
84888285113
-
An integrated bioinformatics approach to the discovery of cis-regulatory elements involved in plant gravitropic signal transduction
-
Liang X, Shen K, Lichtenberg J, Wyatt SE, Welch LR. An integrated bioinformatics approach to the discovery of cis-regulatory elements involved in plant gravitropic signal transduction. International Journal of Computational Bioscience 2010, 1(1):33-54.
-
(2010)
International Journal of Computational Bioscience
, vol.1
, Issue.1
, pp. 33-54
-
-
Liang, X.1
Shen, K.2
Lichtenberg, J.3
Wyatt, S.E.4
Welch, L.R.5
-
28
-
-
78650812664
-
Encyclopedias of DNA elements for Plant Genomes
-
Hackensack: World Scientific Publishing Company; (in press), Elnitski L, Piontkivska H, Welch L
-
Lichtenberg J, Yilmaz A, Kurz K, Liang X, Nelson C, Bitterman T, Stockinger E, Grotewold E, Welch LR. Encyclopedias of DNA elements for Plant Genomes. Advances in Genomic Sequence Analysis and Pattern Discovery 2011, Hackensack: World Scientific Publishing Company; (in press), Elnitski L, Piontkivska H, Welch L.
-
(2011)
Advances in Genomic Sequence Analysis and Pattern Discovery
-
-
Lichtenberg, J.1
Yilmaz, A.2
Kurz, K.3
Liang, X.4
Nelson, C.5
Bitterman, T.6
Stockinger, E.7
Grotewold, E.8
Welch, L.R.9
-
29
-
-
0347492019
-
AGRIS Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors
-
10.1186/1471-2105-4-25, 166152, 12820902
-
Davaluri RV, Sun H, Palaniswamy SK, Matthews N, Molina C, Kurtz M, Grotewold E. AGRIS Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics 2003, 4(1):25. 10.1186/1471-2105-4-25, 166152, 12820902.
-
(2003)
BMC Bioinformatics
, vol.4
, Issue.1
, pp. 25
-
-
Davaluri, R.V.1
Sun, H.2
Palaniswamy, S.K.3
Matthews, N.4
Molina, C.5
Kurtz, M.6
Grotewold, E.7
-
30
-
-
84888285058
-
An Open Source Framework for Bioinformatics Word Enumeration and Scoring
-
Kurz K, Lichtenberg J, Nau L, Drews F, Welch LR. An Open Source Framework for Bioinformatics Word Enumeration and Scoring. 10th Annual Bioinformatics Open Source Conference BOSC: 27-28 June 2009; Stockholm 2009, 37.
-
(2009)
10th Annual Bioinformatics Open Source Conference BOSC: 27-28 June 2009; Stockholm
, pp. 37
-
-
Kurz, K.1
Lichtenberg, J.2
Nau, L.3
Drews, F.4
Welch, L.R.5
-
31
-
-
78650823303
-
A Parallel, High-Throughput Framework for Discovery of DNA Motifs
-
Ohio University Electrical Engineering and Computer Science
-
Kurz K. A Parallel, High-Throughput Framework for Discovery of DNA Motifs. 2010, Ohio University Electrical Engineering and Computer Science.
-
(2010)
-
-
Kurz, K.1
-
32
-
-
25844465842
-
Practical methods for constructing suffix trees
-
Tian Y, Tata S, Hankins RA, Patel JM. Practical methods for constructing suffix trees. The VLDB Journal 2005, 14(3):281-299.
-
(2005)
The VLDB Journal
, vol.14
, Issue.3
, pp. 281-299
-
-
Tian, Y.1
Tata, S.2
Hankins, R.A.3
Patel, J.M.4
-
33
-
-
76549127379
-
Scalable parallel word search in multicore/multiprocessor systems
-
Drews F, Lichtenberg J, Welch L. Scalable parallel word search in multicore/multiprocessor systems. J Supercomput 2010, 51:58-75.
-
(2010)
J Supercomput
, vol.51
, pp. 58-75
-
-
Drews, F.1
Lichtenberg, J.2
Welch, L.3
-
34
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
10.1038/nbt1053, 15637633
-
Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, et al. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology 2005, 23:137-144. 10.1038/nbt1053, 15637633.
-
(2005)
Nature Biotechnology
, vol.23
, pp. 137-144
-
-
Tompa, M.1
Li, N.2
Bailey, T.L.3
Church, G.M.4
De Moor, B.5
Eskin, E.6
Favorov, A.V.7
Frith, M.C.8
Fu, Y.9
Kent, W.J.10
-
35
-
-
70350429218
-
The Plant Genome: Decoding the Transcriptional Hardwiring
-
Grotewold E, Springer N. The Plant Genome: Decoding the Transcriptional Hardwiring. Annual Plant Reviews 2009, 35:196-227.
-
(2009)
Annual Plant Reviews
, vol.35
, pp. 196-227
-
-
Grotewold, E.1
Springer, N.2
|