-
1
-
-
84963563106
-
Visualization Challenges for a New Cyberpharmaceutical Computing Paradigm
-
Turner, R.J., K. Chaturvedi, N.J. Edwards, D. Fasulo, A.L. Halpern, D.H. Huson, O. Kohlbacher, J.R. Miller, K. Reinert, and K.A. Remington. Visualization Challenges for a New Cyberpharmaceutical Computing Paradigm. in Parallel and large-data visualization and graphics: Proceedings of the IEEE 2001 symposium on parallel and large-data visualization and graphics. 2001.
-
(2001)
Parallel and large-data visualization and graphics: Proceedings of the IEEE 2001 symposium on parallel and large-data visualization and graphics
-
-
Turner, R.J.1
Chaturvedi, K.2
Edwards, N.J.3
Fasulo, D.4
Halpern, A.L.5
Huson, D.H.6
Kohlbacher, O.7
Miller, J.R.8
Reinert, K.9
Remington, K.A.10
-
2
-
-
0005008911
-
Visualization for Bio-and Chem-informatics: Are you being served?
-
IEEE Computer Society Washington, DC, USA
-
Lee, J.P., C. Ahlberg, D. Carr, G. Grinstein, J. Kinney, and J. Saffer. Visualization for Bio-and Chem-informatics: are you being served? in Proceedings of the conference on Visualization'01. 2001: IEEE Computer Society Washington, DC, USA.
-
(2001)
Proceedings of the conference on Visualization'01
-
-
Lee, J.P.1
Ahlberg, C.2
Carr, D.3
Grinstein, G.4
Kinney, J.5
Saffer, J.6
-
3
-
-
0036709197
-
The Next Frontier for Bio-and Cheminformatics Visualization. Computer Graphics and Applications
-
Lee, J.P., D. Carr, G. Grinstein, J. Kinney, and J. Saffer, The Next Frontier for Bio-and Cheminformatics Visualization. Computer Graphics and Applications, IEEE, 2002. 22(5): p. 6-11.
-
IEEE, 2002
, vol.22
, Issue.5
, pp. 6-11
-
-
Lee, J.P.1
Carr, D.2
Grinstein, G.3
Kinney, J.4
Saffer, J.5
-
4
-
-
33746358199
-
Visualization research challenges - A report summary
-
Moorhead, R., C. Johnson, T. Munzner, H. Pfister, P. Rheingans, and T.S. Yoo, Visualization research challenges - A report summary. Computing in Science & Engineering, 2006. 8(4): p. 66-73.
-
(2006)
Computing in Science & Engineering
, vol.8
, Issue.4
, pp. 66-73
-
-
Moorhead, R.1
Johnson, C.2
Munzner, T.3
Pfister, H.4
Rheingans, P.5
Yoo, T.S.6
-
5
-
-
33645237140
-
NIH-NSF Visualization Research Challenges report summary
-
Munzner, T., C. Johnson, R. Moorhead, H. Pfister, P. Rheingans, and T.S. Yoo, NIH-NSF Visualization Research Challenges report summary. Ieee Computer Graphics and Applications, 2006. 26(2): p. 20-24.
-
(2006)
Ieee Computer Graphics and Applications
, vol.26
, Issue.2
, pp. 20-24
-
-
Munzner, T.1
Johnson, C.2
Moorhead, R.3
Pfister, H.4
Rheingans, P.5
Yoo, T.S.6
-
6
-
-
70350349277
-
Vis keynote address - Visualization challenges at the intersection of petascale computing and biological science
-
Stevens, R., Vis keynote address - Visualization challenges at the intersection of petascale computing and biological science. Ieee Transactions on Visualization and Computer Graphics, 2007. 13(6): p. Xxiv-Xxiv.
-
(2007)
Ieee Transactions on Visualization and Computer Graphics
, vol.13
, Issue.6
-
-
Stevens, R.1
-
7
-
-
0034447725
-
Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems
-
Schilling, C.H., J.S. Edwards, D. Letscher, and B.O. Palsson, Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnol Bioeng, 2000. 71(4): p. 286-306.
-
(2000)
Biotechnol Bioeng
, vol.71
, Issue.4
, pp. 286-306
-
-
Schilling, C.H.1
Edwards, J.S.2
Letscher, D.3
Palsson, B.O.4
-
8
-
-
45449099820
-
Comparing Assemblies Using Fragments and Mate-Pairs
-
Springer-Verlag London, UK
-
Huson, D.H., A.L. Halpern, Z. Lai, E.W. Myers, K. Reinert, and G.G. Sutton. Comparing Assemblies Using Fragments and Mate-Pairs. in Proceedings of the First International Workshop on Algorithms in Bioinformatics. 2001: Springer-Verlag London, UK.
-
(2001)
Proceedings of the First International Workshop on Algorithms in Bioinformatics
-
-
Huson, D.H.1
Halpern, A.L.2
Lai, Z.3
Myers, E.W.4
Reinert, K.5
Sutton, G.G.6
-
9
-
-
0031955274
-
BioViews: Java-Based Tools for Genomic Data Visualization
-
Cold Spring Harbor Lab
-
Helt, G.A., S. Lewis, A.E. Loraine, and G.M. Rubin, BioViews: Java-Based Tools for Genomic Data Visualization. Genome Res. 1998: Cold Spring Harbor Lab. 291-305.
-
(1998)
Genome Res
, pp. 291-305
-
-
Helt, G.A.1
Lewis, S.2
Loraine, A.E.3
Rubin, G.M.4
-
10
-
-
0031742286
-
Zomit: Biological data visualization and browsing
-
Pook, S., Zomit: biological data visualization and browsing. Bioinformatics, 1998. 14(9): p. 807-814.
-
(1998)
Bioinformatics
, vol.14
, Issue.9
, pp. 807-814
-
-
Pook, S.1
-
11
-
-
0032919060
-
The HuGeMap Database: Interconnection and visualization of human genome maps
-
Barillot, E., S. Pook, F. Guyon, C. Cussat-Blanc, E. Viara, and G. Vaysseix, The HuGeMap Database: interconnection and visualization of human genome maps. Nucleic Acids Research. 27(1): p. 119-122.
-
Nucleic Acids Research
, vol.27
, Issue.1
, pp. 119-122
-
-
Barillot, E.1
Pook, S.2
Guyon, F.3
Cussat-Blanc, C.4
Viara, E.5
Vaysseix, G.6
-
12
-
-
2942609356
-
Visualizing the genome: Techniques for presenting human genome data and annotations
-
Loraine, A.E. and G.A. Helt, Visualizing the genome: techniques for presenting human genome data and annotations. BMC Bioinformatics, 2002. 3(1): p. 19-19.
-
(2002)
BMC Bioinformatics
, vol.3
, Issue.1
, pp. 19-19
-
-
Loraine, A.E.1
Helt, G.A.2
-
13
-
-
1842507574
-
Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments
-
Shah, N., O. Couronne, L.A. Pennacchio, M. Brudno, S. Batzoglou, E.W. Bethel, E.M. Rubin, B. Hamann, and I. Dubchak, Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics, 2004. 20: p. 636-643.
-
(2004)
Bioinformatics
, vol.20
, pp. 636-643
-
-
Shah, N.1
Couronne, O.2
Pennacchio, L.A.3
Brudno, M.4
Batzoglou, S.5
Bethel, E.W.6
Rubin, E.M.7
Hamann, B.8
Dubchak, I.9
-
14
-
-
0034518158
-
visualizing global DNA sequence alignments of arbitrary length
-
VISTA
-
Mayor, C., M. Brudno, J.R. Schwartz, A. Poliakov, E.M. Rubin, K.A. Frazer, L.S. Pachter, and I. Dubchak, VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics, 2000. 16: p. 1046-1047.
-
(2000)
Bioinformatics
, vol.16
, pp. 1046-1047
-
-
Mayor, C.1
Brudno, M.2
Schwartz, J.R.3
Poliakov, A.4
Rubin, E.M.5
Frazer, K.A.6
Pachter, L.S.7
Dubchak, I.8
-
15
-
-
0012306021
-
Apollo: A sequence annotation editor
-
Lewis, S.E., S.M.J. Searle, N. Harris, M. Gibson, V. Iyer, J. Richter, C. Wiel, L. Bayraktaroglu, E. Birney, and M.A. Crosby, Apollo: a sequence annotation editor. Genome Biology, 2002. 3(12): p. 1-14.
-
(2002)
Genome Biology
, vol.3
, Issue.12
, pp. 1-14
-
-
Lewis, S.E.1
Searle, S.M.J.2
Harris, N.3
Gibson, M.4
Iyer, V.5
Richter, J.6
Wiel, C.7
Bayraktaroglu, L.8
Birney, E.9
Crosby, M.A.10
-
16
-
-
1842611935
-
Java-based application framework for visualization of gene regulatory region annotations
-
Sun, H. and R.V. Davuluri, Java-based application framework for visualization of gene regulatory region annotations. Bioinformatics, 2004. 20: p. 727-734.
-
(2004)
Bioinformatics
, vol.20
, pp. 727-734
-
-
Sun, H.1
Davuluri, R.V.2
-
17
-
-
0029654258
-
A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis
-
Sonnhammer, E.L.L. and R. Durbin, A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene, 1995. 167(1-2).
-
(1995)
Gene
, vol.167
, Issue.1-2
-
-
Sonnhammer, E.L.L.1
Durbin, R.2
-
18
-
-
0034020416
-
PipMaker-A Web Server for Aligning Two Genomic DNA Sequences
-
Schwartz, S., Z. Zhang, K.A. Frazer, A. Smit, C. Riemer, J. Bouck, R. Gibbs, R. Hardison, and W. Miller, PipMaker-A Web Server for Aligning Two Genomic DNA Sequences. Genome Research, 2000. 10: p. 577-586.
-
(2000)
Genome Research
, vol.10
, pp. 577-586
-
-
Schwartz, S.1
Zhang, Z.2
Frazer, K.A.3
Smit, A.4
Riemer, C.5
Bouck, J.6
Gibbs, R.7
Hardison, R.8
Miller, W.9
-
19
-
-
1542714627
-
Chromo Wheel: A new spin on eukaryotic chromosome visualization
-
Ekdahl, S. and E.L.L. Sonnhammer, Chromo Wheel: a new spin on eukaryotic chromosome visualization. Bioinformatics, 2004. 20: p. 576-577.
-
(2004)
Bioinformatics
, vol.20
, pp. 576-577
-
-
Ekdahl, S.1
Sonnhammer, E.L.L.2
-
20
-
-
7944238738
-
Information visualization techniques in bioinformatics during the postgenomic era
-
Tao, Y., Y. Liu, C. Friedman, and Y.A. Lussier, Information visualization techniques in bioinformatics during the postgenomic era. Drug Discovery Today: Biosilico, 2004. 2(6): p. 237-245.
-
(2004)
Drug Discovery Today: Biosilico
, vol.2
, Issue.6
, pp. 237-245
-
-
Tao, Y.1
Liu, Y.2
Friedman, C.3
Lussier, Y.A.4
-
21
-
-
0142056169
-
An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges
-
Chain, P., S. Kurtz, E. Ohlebusch, and T. Slezak, An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges. Briefings in Bioinformatics, 2003. 4(2): p. 105-123.
-
(2003)
Briefings in Bioinformatics
, vol.4
, Issue.2
, pp. 105-123
-
-
Chain, P.1
Kurtz, S.2
Ohlebusch, E.3
Slezak, T.4
-
22
-
-
0032441150
-
Cluster Analysis and Display of Genome-Wide Expression Patterns
-
Eisen, M.B., P.T. Spellman, P.O. Brown, and D. Botstein, Cluster Analysis and Display of Genome-Wide Expression Patterns. 1998: National Acad Sciences. 14863-14868.
-
(1998)
National Acad Sciences
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
23
-
-
0036645183
-
Interactively Exploring Hierarchical Clustering Results
-
Seo, J. and B. Shneiderman, Interactively Exploring Hierarchical Clustering Results. IEEE Computer, 2002. 35(7): p. 80-86.
-
(2002)
IEEE Computer
, vol.35
, Issue.7
, pp. 80-86
-
-
Seo, J.1
Shneiderman, B.2
-
24
-
-
70350400024
-
-
Hierarchical Clustering Explorer, University of Maryland: Human-Computer Interaction Laboratory
-
Hierarchical Clustering Explorer, University of Maryland: Human-Computer Interaction Laboratory.
-
-
-
-
25
-
-
70350359229
-
-
GeneSpring, http://www.chem.agilent.com/en-US/Products/software/ lifesciencesinformatics/genespringgx/Pages/default.aspx.
-
GeneSpring
-
-
-
26
-
-
70350362120
-
-
Spotfire, http://spotfire.tibco.com/.
-
Spotfire
-
-
-
27
-
-
0034069495
-
Gene ontology: Tool for the Unification of Biology
-
Ashburner, M., C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, and J.T. Eppig, Gene ontology: Tool for the Unification of Biology. Nature Genetics, 2000. 25(1): p. 25-29.
-
(2000)
Nature Genetics
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
28
-
-
33749412013
-
A PCA Based Method of Gene Expression Visual Analysis
-
Nishimura, K., K. Abe, S. Ishikawa, S. Tsutsumi, K. Hirota, H. Aburatani, and M. Hirose, A PCA Based Method of Gene Expression Visual Analysis. Genome Informatics Series, 2003. 14: p. 346-347.
-
(2003)
Genome Informatics Series
, vol.14
, pp. 346-347
-
-
Nishimura, K.1
Abe, K.2
Ishikawa, S.3
Tsutsumi, S.4
Hirota, K.5
Aburatani, H.6
Hirose, M.7
-
29
-
-
25444458348
-
GO Based Data Mining Tool for Characteristic Attribute Interpretation on a Group of Biological Entities
-
GOODIES
-
Lee, S.G., W.S. Lee, and Y.S. Kim, GOODIES: GO Based Data Mining Tool for Characteristic Attribute Interpretation on a Group of Biological Entities. Genome Informatics Series, 2003. 14: p. 675-676.
-
(2003)
Genome Informatics Series
, vol.14
, pp. 675-676
-
-
Lee, S.G.1
Lee, W.S.2
Kim, Y.S.3
-
30
-
-
0035237805
-
Rich Probabilistic Models for Gene Expression
-
Segal, E., B. Taskar, A. Gasch, N. Friedman, and D. Koller, Rich Probabilistic Models for Gene Expression. Bioinformatics, 2001. 17: p. 243-252.
-
(2001)
Bioinformatics
, vol.17
, pp. 243-252
-
-
Segal, E.1
Taskar, B.2
Gasch, A.3
Friedman, N.4
Koller, D.5
-
31
-
-
0036187914
-
information visualization for annotated microarray data
-
DRAGON View
-
Bouton, C. and J. Pevsner, DRAGON View: information visualization for annotated microarray data. Bioinformatics, 2002. 18: p. 323-324.
-
(2002)
Bioinformatics
, vol.18
, pp. 323-324
-
-
Bouton, C.1
Pevsner, J.2
-
32
-
-
3242882895
-
-
Herrero, J., J.M. Vaquerizas, F. Al-Shahrour, L. Conde, A. Mateos, J.S.R. Diaz-Uriarte, and J. Dopazo, New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Research, 2004. 32(Web Server Issue): p. W485-W485.
-
Herrero, J., J.M. Vaquerizas, F. Al-Shahrour, L. Conde, A. Mateos, J.S.R. Diaz-Uriarte, and J. Dopazo, New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Research, 2004. 32(Web Server Issue): p. W485-W485.
-
-
-
-
33
-
-
2442690357
-
Chromo Viz: Visualization of gene expression data onto chromosomes using scalable vector graphics
-
Kim, J., H.J. Chung, C.H. Park, W.Y. Park, and J.H. Kim, Chromo Viz: visualization of gene expression data onto chromosomes using scalable vector graphics. Bioinformatics, 2004. 20: p. 1191-1192.
-
(2004)
Bioinformatics
, vol.20
, pp. 1191-1192
-
-
Kim, J.1
Chung, H.J.2
Park, C.H.3
Park, W.Y.4
Kim, J.H.5
-
34
-
-
0242490780
-
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
-
Shannon, P., A. Markiel, O. Ozier, N.S. Baliga, J.T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker, Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. 2003: Genome Res. 2498-2504.
-
(2003)
Genome Res
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
35
-
-
0037264280
-
Osprey: A Network Visualization System
-
Breitkreutz, B.J., C. Stark, and M. Tyers, Osprey: A Network Visualization System. Genome Biol, 2003. 4(3): p. R22-R22.
-
(2003)
Genome Biol
, vol.4
, Issue.3
-
-
Breitkreutz, B.J.1
Stark, C.2
Tyers, M.3
-
36
-
-
25444482839
-
Pathway Voyager: Pathway Mapping Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Database
-
Altermann, E. and T.R. Klaenhammer, Pathway Voyager: Pathway Mapping Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Database. BMC Genomics, 2005. 6(1): p. 60-60.
-
(2005)
BMC Genomics
, vol.6
, Issue.1
, pp. 60-60
-
-
Altermann, E.1
Klaenhammer, T.R.2
-
37
-
-
70350365967
-
-
Reactome, European Bioinformatics Institute, and GO Consortium: Cold Spring Harbor Laboratory
-
Reactome, European Bioinformatics Institute, and GO Consortium: Cold Spring Harbor Laboratory.
-
-
-
-
38
-
-
70350380229
-
-
OmniViz, http://www.omniviz.com/.
-
OmniViz
-
-
-
39
-
-
33751333696
-
Visualization of complementary systems biology data with parallel heatmaps
-
Podowski, R.M., B. Miller, and W.W. Wasserman, Visualization of complementary systems biology data with parallel heatmaps. Systems Biology, 2006. 50(6).
-
(2006)
Systems Biology
, vol.50
, Issue.6
-
-
Podowski, R.M.1
Miller, B.2
Wasserman, W.W.3
-
40
-
-
16244392292
-
A Model and Software System for Coordinated and Multiple Views in Exploratory Visualization
-
Boukhelifa, N. and P.J. Rodgers, A Model and Software System for Coordinated and Multiple Views in Exploratory Visualization. Information Visualization, 2003. 2(4): p. 258-269.
-
(2003)
Information Visualization
, vol.2
, Issue.4
, pp. 258-269
-
-
Boukhelifa, N.1
Rodgers, P.J.2
-
41
-
-
70350359223
-
-
Proceedings of the 2nd International Conference on Coordinated and Multiple Views in Exploratory Visualization. 2004. London, England.
-
Proceedings of the 2nd International Conference on Coordinated and Multiple Views in Exploratory Visualization. 2004. London, England.
-
-
-
-
42
-
-
85008053984
-
-
Min Chen, David Ebert, Hans Hagen, Robert S. Laramee, Robert van Liere, Kwan-Liu Ma, William Ribarsky, and G. Scheuermann, Data, Information, and Knowledge in Visualization. IEEE Computer Graphics and Applications, 2009.
-
Min Chen, David Ebert, Hans Hagen, Robert S. Laramee, Robert van Liere, Kwan-Liu Ma, William Ribarsky, and G. Scheuermann, Data, Information, and Knowledge in Visualization. IEEE Computer Graphics and Applications, 2009.
-
-
-
-
43
-
-
65549151293
-
-
Samatova, N.F., M.C. Schmidt, W. Hendrix, P. Breimyer, K. Thomas, and B.H. Park. Coupling graph perturbation theory with scalable parallel algorithms for large-scale enumeration of maximal cliques in biological graphs. in Journal of Physics: Conference Series. 2008: Institute of Physics Publishing.
-
Samatova, N.F., M.C. Schmidt, W. Hendrix, P. Breimyer, K. Thomas, and B.H. Park. Coupling graph perturbation theory with scalable parallel algorithms for large-scale enumeration of maximal cliques in biological graphs. in Journal of Physics: Conference Series. 2008: Institute of Physics Publishing.
-
-
-
-
44
-
-
70350362119
-
-
NCBI, National Center for Biotechnology Information, http://www.ncbi.nlm. nih.gov.
-
NCBI, National Center for Biotechnology Information, http://www.ncbi.nlm. nih.gov.
-
-
-
-
45
-
-
38349190229
-
The Tree of Life Web Project
-
Maddison, D.R. and K.S. Schulz, The Tree of Life Web Project. Zootaxa, 2007. 1668: p. 19-40.
-
(2007)
Zootaxa
, vol.1668
, pp. 19-40
-
-
Maddison, D.R.1
Schulz, K.S.2
-
47
-
-
77953998482
-
-
Munzner, T., F. Guimbretiere, S. Tasiran, L. Zhang, and Y. Zhou, TreeJuxtaposer: Scalable Tree Comparison using Focus+ Context with Guaranteed Visibility. SIGGRAPH, 2003.
-
(2003)
TreeJuxtaposer: Scalable Tree Comparison using Focus+ Context with Guaranteed Visibility. SIGGRAPH
-
-
Munzner, T.1
Guimbretiere, F.2
Tasiran, S.3
Zhang, L.4
Zhou, Y.5
-
48
-
-
27144532729
-
Phylogenetic Trees: An Information Visualisation Perspective
-
Australian Computer Society, Inc. Darlinghurst, Australia, Australia
-
Carrizo, S.F. Phylogenetic Trees: An Information Visualisation Perspective. in Proceedings of the second conference on Asia-Pacific bioinformatics-Volume 29. 2004: Australian Computer Society, Inc. Darlinghurst, Australia, Australia.
-
(2004)
Proceedings of the second conference on Asia-Pacific bioinformatics
, vol.29
-
-
Carrizo, S.F.1
-
50
-
-
70350382823
-
-
PHYLIP, http://evolution.genetics.washington.edu/phylip/software.html.
-
PHYLIP, http://evolution.genetics.washington.edu/phylip/software.html.
-
-
-
-
51
-
-
0035861456
-
Bayesian Inference of Phylogeny and Its Impact on Evolutionary
-
Huelsenbeck, J.P., F. Ronquist, R. Nielsen, and J.P. Bollback, Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology. Science, 2001. 294 (5550): p. 2310-2314.
-
(2001)
Biology. Science
, vol.294
, Issue.5550
, pp. 2310-2314
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
Nielsen, R.3
Bollback, J.P.4
-
52
-
-
85129670957
-
Parallel implementation and performance of fastDNAml - a program for maximum likelihood phylogenetic inference
-
Stewart, C.A., D. Hart, D.K. Berry, G.J. Olsen, E.A. Wernert, and W. Fischer. Parallel implementation and performance of fastDNAml - a program for maximum likelihood phylogenetic inference. in Proceedings of SC2001. 2001.
-
(2001)
Proceedings of SC2001
-
-
Stewart, C.A.1
Hart, D.2
Berry, D.K.3
Olsen, G.J.4
Wernert, E.A.5
Fischer, W.6
-
54
-
-
25444497721
-
libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny
-
Butt, D., A.J. Roger, and C. Blouin, libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny. BMC Bioinformatics, 2005. 6: p. 138-138.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 138-138
-
-
Butt, D.1
Roger, A.J.2
Blouin, C.3
-
55
-
-
0003991673
-
-
Sinauer Associates Sunderland, Mass, USA
-
Felsenstein, J., Inferring phylogenies. 2003: Sinauer Associates Sunderland, Mass., USA.
-
(2003)
Inferring phylogenies
-
-
Felsenstein, J.1
-
56
-
-
0033499153
-
Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima
-
Goloboff, P.A., Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima. Cladistics, 1999. 15(4): p. 415-428.
-
(1999)
Cladistics
, vol.15
, Issue.4
, pp. 415-428
-
-
Goloboff, P.A.1
-
57
-
-
14644397888
-
RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees
-
Stamatakis, A., T. Ludwig, and H. Meier, RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics, 2005. 21: p. 456-463.
-
(2005)
Bioinformatics
, vol.21
, pp. 456-463
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
58
-
-
70350350456
-
-
* and Other Methods, Version 4. Sunderland, MA: Sinauer Associates, 1998
-
* and Other Methods). Version 4. Sunderland, MA: Sinauer Associates, 1998.
-
-
-
-
60
-
-
0034316981
-
An initial examination of ease of use for 2D and 3D information visualizations of web content
-
Risden, K., M.P. Czerwinski, T. Munzner, and D.B. Cook, An initial examination of ease of use for 2D and 3D information visualizations of web content. International Journal of Human-Computers Studies, 2000. 53(5): p. 695-714.
-
(2000)
International Journal of Human-Computers Studies
, vol.53
, Issue.5
, pp. 695-714
-
-
Risden, K.1
Czerwinski, M.P.2
Munzner, T.3
Cook, D.B.4
-
62
-
-
84957864798
-
Drawing Large Graphs with H3Viewer and Site Manager
-
Munzner, T., Drawing Large Graphs with H3Viewer and Site Manager. Lecture Notes in Computer Science, 1998 (1547): p. 384-393.
-
(1547)
Lecture Notes in Computer Science
, pp. 384-393
-
-
Munzner, T.1
-
63
-
-
0032121774
-
-
Munzner, T., Exploring large graphs in 3D hyperbolic space. Computer Graphics and Applications, IEEE, 1998. 18(4): p. 18-23.
-
Munzner, T., Exploring large graphs in 3D hyperbolic space. Computer Graphics and Applications, IEEE, 1998. 18(4): p. 18-23.
-
-
-
-
64
-
-
70350382819
-
-
Felsenstein, J, PHYLIP, phylogeny inference package (version 3.2, Cladistics, 1989. 51, p. 164-166
-
Felsenstein, J., PHYLIP - phylogeny inference package (version 3.2). Cladistics, 1989. 5(1): p. 164-166.
-
-
-
-
66
-
-
45149111660
-
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
-
Feist, A.M. and B.O. Palsson, The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nature Biotechnology, 2008. 26(6): p. 659-667.
-
(2008)
Nature Biotechnology
, vol.26
, Issue.6
, pp. 659-667
-
-
Feist, A.M.1
Palsson, B.O.2
-
67
-
-
40549120596
-
The RAST Server: Rapid Annotations using Subsystems Technology
-
Aziz, R.K., D. Bartels, A.A. Best, M. DeJongh, T. Disz, R.A. Edwards, K. Formsma, S. Gerdes, E.M. Glass, and M. Kubal, The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics, 2008. 9: p. 75-75.
-
(2008)
BMC Genomics
, vol.9
, pp. 75-75
-
-
Aziz, R.K.1
Bartels, D.2
Best, A.A.3
DeJongh, M.4
Disz, T.5
Edwards, R.A.6
Formsma, K.7
Gerdes, S.8
Glass, E.M.9
Kubal, M.10
-
68
-
-
34248632008
-
Toward the automated generation of genome-scale metabolic networks in the SEED
-
DeJongh, M., K. Formsma, P. Boillot, J. Gould, M. Rycenga, A. Best, M.R. Jakobsen, J. Haasnoot, J. Wengel, and B. Berkhout, Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics, 2007. 8(139).
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.139
-
-
DeJongh, M.1
Formsma, K.2
Boillot, P.3
Gould, J.4
Rycenga, M.5
Best, A.6
Jakobsen, M.R.7
Haasnoot, J.8
Wengel, J.9
Berkhout, B.10
-
69
-
-
54449092307
-
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: IJN746 as a cell factory
-
Nogales, J., B.O. Palsson, and I. Thiele, A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Systems Biology, 2008. 2(1): p. 79-79.
-
(2008)
BMC Systems Biology
, vol.2
, Issue.1
, pp. 79-79
-
-
Nogales, J.1
Palsson, B.O.2
Thiele, I.3
-
70
-
-
51849115840
-
Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network
-
Lee, J., H. Yun, A.M. Feist, B.O. Palsson, and S.Y. Lee, Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Applied Microbiology and Biotechnology, 2008. 80(5): p. 849-862.
-
(2008)
Applied Microbiology and Biotechnology
, vol.80
, Issue.5
, pp. 849-862
-
-
Lee, J.1
Yun, H.2
Feist, A.M.3
Palsson, B.O.4
Lee, S.Y.5
-
71
-
-
33749547956
-
Comparative Genomics and Experimental Characterization of N-Acetylglucosamine Utilization Pathway of Shewanella oneidensis
-
Yang, C., D.A. Rodionov, X. Li, O.N. Laikova, M.S. Gelfand, O.P. Zagnitko, M.F. Romine, A.Y. Obraztsova, K.H. Nealson, and A.L. Osterman, Comparative Genomics and Experimental Characterization of N-Acetylglucosamine Utilization Pathway of Shewanella oneidensis. Journal of Biological Chemistry, 2006. 281(40): p. 29872-29872.
-
(2006)
Journal of Biological Chemistry
, vol.281
, Issue.40
, pp. 29872-29872
-
-
Yang, C.1
Rodionov, D.A.2
Li, X.3
Laikova, O.N.4
Gelfand, M.S.5
Zagnitko, O.P.6
Romine, M.F.7
Obraztsova, A.Y.8
Nealson, K.H.9
Osterman, A.L.10
-
72
-
-
0037021804
-
Characterizing the metabolic phenotype: A phenotype phase plane analysis
-
Edwards, J.S., R. Ramakrishna, and B.O. Palsson, Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol Bioeng, 2002. 77(1): p. 27-36.
-
(2002)
Biotechnol Bioeng
, vol.77
, Issue.1
, pp. 27-36
-
-
Edwards, J.S.1
Ramakrishna, R.2
Palsson, B.O.3
-
73
-
-
0035047834
-
Genotype-phenotype interactions in Wilson's disease: Insight from an Icelandic mutation
-
Palsson, R., J.G. Jonasson, M. Kristjansson, A. Bodvarsson, R.D. Goldin, D.W. Cox, and S. Olafsson, Genotype-phenotype interactions in Wilson's disease: insight from an Icelandic mutation. Eur J Gastroenterol Hepatol, 2001. 13(4): p. 433-6.
-
(2001)
Eur J Gastroenterol Hepatol
, vol.13
, Issue.4
, pp. 433-436
-
-
Palsson, R.1
Jonasson, J.G.2
Kristjansson, M.3
Bodvarsson, A.4
Goldin, R.D.5
Cox, D.W.6
Olafsson, S.7
-
74
-
-
0033136116
-
Toward metabolic phenomics: Analysis of genomic data using flux balances
-
Schilling, C.H., J.S. Edwards, and B.O. Palsson, Toward metabolic phenomics: analysis of genomic data using flux balances. Biotechnol Prog, 1999. 15(3): p. 288-95.
-
(1999)
Biotechnol Prog
, vol.15
, Issue.3
, pp. 288-295
-
-
Schilling, C.H.1
Edwards, J.S.2
Palsson, B.O.3
-
75
-
-
0242559054
-
Pathway studio-the analysis and navigation of molecular networks
-
Nikitin, A., S. Egorov, N. Daraselia, and I. Mazo, Pathway studio-the analysis and navigation of molecular networks. Bioinformatics, 2003. 19: p. 2155-2157.
-
(2003)
Bioinformatics
, vol.19
, pp. 2155-2157
-
-
Nikitin, A.1
Egorov, S.2
Daraselia, N.3
Mazo, I.4
-
76
-
-
70350369818
-
-
Osprey, http://biodata.mshri.on.ca/osprey/index.html.
-
Osprey
-
-
-
77
-
-
32144455205
-
Patika web: A Web interface for analyzing biological pathways through advanced querying and visualization
-
Dogrusoz, U., E.Z. Erson, E. Giral, E. Demir, O. Babur, A. Cetintas, and R. Colak, Patika web: a Web interface for analyzing biological pathways through advanced querying and visualization. Bioinformatics, 2006. 22: p. 374-375.
-
(2006)
Bioinformatics
, vol.22
, pp. 374-375
-
-
Dogrusoz, U.1
Erson, E.Z.2
Giral, E.3
Demir, E.4
Babur, O.5
Cetintas, A.6
Colak, R.7
-
78
-
-
2942609149
-
an online visualization and analysis tool for biological interaction data
-
VisANT
-
Hu, Z., J. Mellor, J. Wu, and C. DeLisi, VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics, 2004. 5(1): p. 17-17.
-
(2004)
BMC Bioinformatics
, vol.5
, Issue.1
, pp. 17-17
-
-
Hu, Z.1
Mellor, J.2
Wu, J.3
DeLisi, C.4
-
79
-
-
13444309633
-
ProViz: Protein interaction visualization and exploration
-
Iragne, F., M. Nikolski, B. Mathieu, D. Auber, and D. Sherman, ProViz: protein interaction visualization and exploration. Bioinformatics, 2005. 21: p. 272-274.
-
(2005)
Bioinformatics
, vol.21
, pp. 272-274
-
-
Iragne, F.1
Nikolski, M.2
Mathieu, B.3
Auber, D.4
Sherman, D.5
-
80
-
-
33644656793
-
Systematic identification of functional orthologs based on protein network comparison
-
Bandyopadhyay, S., R. Sharan, and T. Ideker, Systematic identification of functional orthologs based on protein network comparison. Genome Res, 2006. 16(3): p. 428-35.
-
(2006)
Genome Res
, vol.16
, Issue.3
, pp. 428-435
-
-
Bandyopadhyay, S.1
Sharan, R.2
Ideker, T.3
-
81
-
-
0141593601
-
Conserved pathways within bacteria and yeast as revealed by global protein network alignment
-
Kelley, B.P., R. Sharan, R.M. Karp, T. Sittler, D.E. Root, B.R. Stockwell, and T. Ideker, Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci USA, 2003. 100(20): p. 11394-9.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.20
, pp. 11394-11399
-
-
Kelley, B.P.1
Sharan, R.2
Karp, R.M.3
Sittler, T.4
Root, D.E.5
Stockwell, B.R.6
Ideker, T.7
-
82
-
-
33748257786
-
Graemlin: General and robust alignment of multiple large interaction networks
-
Flannick, J., A. Novak, B.S. Srinivasan, H.H. McAdams, and S. Batzoglou, Graemlin: general and robust alignment of multiple large interaction networks. Genome Res, 2006. 16(9): p. 1169-81.
-
(2006)
Genome Res
, vol.16
, Issue.9
, pp. 1169-1181
-
-
Flannick, J.1
Novak, A.2
Srinivasan, B.S.3
McAdams, H.H.4
Batzoglou, S.5
-
83
-
-
33645985807
-
Pairwise alignment of protein interaction networks
-
Koyuturk, M., Y. Kim, U. Topkara, S. Subramaniam, W. Szpankowski, and A. Grama, Pairwise alignment of protein interaction networks. J Comput Biol, 2006. 13(2): p. 182-99.
-
(2006)
J Comput Biol
, vol.13
, Issue.2
, pp. 182-199
-
-
Koyuturk, M.1
Kim, Y.2
Topkara, U.3
Subramaniam, S.4
Szpankowski, W.5
Grama, A.6
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