Søren Brunak

2008
44	EE	Nicholas Paul Gauthier, Malene Erup Larsen, Rasmus Wernersson, Ulrik de Lichtenberg, Lars Juhl Jensen, Søren Brunak, Thomas Skøt Jensen: Cyclebase.org - a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Research 36(Database-Issue): 854-859 (2008)
2007
43	EE	Frank Panitz, Henrik Stengaard, Henrik Hornshøj, Jan Gorodkin, Jakob Hedegaard, Susanna Cirera, Bo Thomsen, Lone B. Madsen, Anette Høj, Rikke K. Vingborg, Bujie Zahn, Xuegang Wang, Xuefei Wang, Rasmus Wernersson, Claus B. Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J. Nielsen, Jakob Hull Havgaard, Søren Brunak, Merete Fredholm, Christian Bendixen: SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. ISMB/ECCB (Supplement of Bioinformatics) 2007: 387-391
42	EE	Claus Lundegaard, Ole Lund, Can Kesmir, Søren Brunak, Morten Nielsen: Modeling the adaptive immune system: predictions and simulations. Bioinformatics 23(24): 3265-3275 (2007)
2006
41	EE	Philip E. Bourne, Søren Brunak: ISMB 2006. ISMB (Supplement of Bioinformatics) 2006: 1-2
2005
40	EE	Jannick Dyrløv Bendtsen, Henrik Nielsen, David Widdick, Tracy Palmer, Søren Brunak: Prediction of twin-arginine signal peptides. BMC Bioinformatics 6: 167 (2005)
39	EE	Svava Ósk Jónsdóttir, Flemming Steen Jørgensen, Søren Brunak: Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates. Bioinformatics 21(10): 2145-2160 (2005)
38	EE	Ulrik de Lichtenberg, Lars Juhl Jensen, Anders Fausbøll, Thomas Skøt Jensen, Peer Bork, Søren Brunak: Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics 21(7): 1164-1171 (2005)
2004
37	EE	Claus Lundegaard, Morten Nielsen, Kasper Lamberth, Peder Worning, Christina Sylvester-Hvid, Søren Buus, Søren Brunak, Ole Lund: MHC Class I Epitope Binding Prediction Trained on Small Data Sets. ICARIS 2004: 217-225
36		Claus A. F. Andersen, Søren Brunak: Representation of Protein-Sequence Information by Amino Acid Subalphabets. AI Magazine 25(1): 97-104 (2004)
35	EE	Lars Kiemer, Ole Lund, Søren Brunak, Nikolaj Blom: Coronavirus 3CLpro proteinase cleavage sites: Possible relevance to SARS virus pathology. BMC Bioinformatics 5: 72 (2004)
34	EE	Morten Nielsen, Claus Lundegaard, Peder Worning, Christina Sylvester-Hvid, Kasper Lamberth, Søren Buus, Søren Brunak, Ole Lund: Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics 20(9): 1388-1397 (2004)
2003
33	EE	Claus Lundegaard, Thomas Nordahl Petersen, Morten Nielsen, Henrik Bohr, Jakob Bohr, Søren Brunak, Garry Gippert, Ole Lund: Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks. Mathematical Methods for Protein Structure Analysis and Design 2003: 117-122
32		Lars Juhl Jensen, Ramneek Gupta, Hans Henrik Stærfeldt, Søren Brunak: Prediction of human protein function according to Gene Ontology categories. Bioinformatics 19(5): 635-642 (2003)
31	EE	Jens Kaae Christensen, Kasper Lamberth, Morten Nielsen, Claus Lundegaard, Peder Worning, Sanne Lise Lauemøller, Søren Buus, Søren Brunak, Ole Lund: Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach. Neural Computation 15(12): 2931-2942 (2003)
30		Tanja la Cour, Ramneek Gupta, Kristoffer Rapacki, Karen Skriver, Flemming M. Poulsen, Søren Brunak: NESbase version 1.0: a database of nuclear export signals. Nucleic Acids Research 31(1): 393-396 (2003)
2002
29	EE	Ramneek Gupta, Søren Brunak: Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function. Pacific Symposium on Biocomputing 2002: 310-322
28		Jeppe S. Spicker, Friedrik Wikman, Ming-Lan Lu, Carlos Cordon-Cardo, Christopher T. Workman, Torben F. Ørntoft, Søren Brunak, Steen Knudsen: Neural network predicts sequence of TP53 gene based on DNA chip. Bioinformatics 18(8): 1133-1134 (2002)
27	EE	David Ussery, Dikeos Mario Soumpasis, Søren Brunak, Hans Henrik Stærfeldt, Peder Worning, Anders Krogh: Bias of Purine Stretches in Sequenced Chromosomes. Computers & Chemistry 26(5): 531-541 (2002)
2001
26		Søren Brunak, Anders Krogh: ISMB 2001. ISMB (Supplement of Bioinformatics) 2001: 1-4
25		Pierre Baldi, Søren Brunak: Bioethics, Fiction Science, and the Future of Mankind - Session Introduction. Pacific Symposium on Biocomputing 2001
24	EE	Pierre Baldi, Søren Brunak, Paolo Frasconi, Gianluca Pollastri, Giovanni Soda: Bidirectional Dynamics for Protein Secondary Structure Prediction. Sequence Learning 2001: 80-104
23		Pierre-François Baisnée, Pierre Baldi, Søren Brunak, Anders Gorm Pedersen: Flexibility of the genetic code with respect to DNA structure. Bioinformatics 17(3): 237-248 (2001)
22	EE	Jan Gorodkin, Bodil Søgaard, Hanne Bay, Hans Doll, Per Kølster, Søren Brunak: Recognition of Environmental and Genetic Effects on Barley Phenolic Fingerprints by Neural Networks. Computers & Chemistry 25(3): 301-307 (2001)
2000
21		Pierre Baldi, Gianluca Pollastri, Claus A. F. Andersen, Søren Brunak: Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks. ISMB 2000: 25-36
20		Pierre Baldi, Søren Brunak, Yves Chauvin, Claus A. F. Andersen, Henrik Nielsen: Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16(5): 412-424 (2000)
19	EE	Thomas M. Frimurer, Robert Bywater, Lars Nærum, Leif Nørskov Lauritsen, Søren Brunak: Improving the Odds in Discriminating "Drug-like" from "Non Drug-like" Compounds. Journal of Chemical Information and Computer Sciences 40(6): 1315-1324 (2000)
1999
18		Jan Gorodkin, Ole Lund, Claus A. F. Andersen, Søren Brunak: Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints. ISMB 1999: 95-105
17		Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen: Structural basis for triplet repeat disorders: a computational analysis. Bioinformatics 15(11): 918-929 (1999)
16		Pierre Baldi, Søren Brunak, Paolo Frasconi, Giovanni Soda, Gianluca Pollastri: Exploiting the past and the future in protein secondary structure prediction. Bioinformatics 15(11): 937-946 (1999)
15		Jan Gorodkin, Hans Henrik Stærfeldt, Ole Lund, Søren Brunak: MatrixPlot: visualizing sequence constraints. Bioinformatics 15(9): 769-770 (1999)
14	EE	Anders Gorm Pedersen, Pierre Baldi, Yves Chauvin, Søren Brunak: The Biology of Eukaryotic Promoter Prediction - A Review. Computers & Chemistry 23(3-4): 191-207 (1999)
13		Andres Kreegipuu, Nikolaj Blom, Søren Brunak: PhosphoBase, a database of phosphorylation sites: release 2.0. Nucleic Acids Research 27(1): 237-239 (1999)
12		Ramneek Gupta, Hanne Birch, Kristoffer Rapacki, Søren Brunak, Jan E. Hansen: O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins. Nucleic Acids Research 27(1): 370-372 (1999)
1998
11		Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen: Computational Applications of DNA Structural Scales. ISMB 1998: 35-42
10		Nikolaj Blom, Andres Kreegipuu, Søren Brunak: PhosphoBase: a database of phosphorylation sites. Nucleic Acids Research 26(1): 382-386 (1998)
9		Jan E. Hansen, Ole Lund, Jette Nilsson, Kristoffer Rapacki, Søren Brunak: O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins. Nucleic Acids Research 26(1): 387-389 (1998)
1997
8		Jan Gorodkin, Laurie J. Heyer, Søren Brunak, Gary D. Stormo: Displaying the information contents of structural RNA alignments: the structure logos. Computer Applications in the Biosciences 13(6): 583-586 (1997)
7	EE	Henrik Nielsen, Jacob Engelbrecht, Søren Brunak, Gunnar von Heijne: A Neural Network Method for Identification of Prokaryotic and Eukaryotic Signal Peptides and Prediction of their Cleavage Sites. Int. J. Neural Syst. 8(5-6): 581-599 (1997)
6		Jan E. Hansen, Ole Lund, Kristoffer Rapacki, Søren Brunak: O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins. Nucleic Acids Research 25(1): 278-282 (1997)
1996
5		Anders Gorm Pedersen, Pierre Baldi, Søren Brunak, Yves Chauvin: Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models. ISMB 1996: 182-191
4		Jan E. Hansen, Ole Lund, Jens O. Nielsen, John-E. S. Hansen, Søren Brunak: O-GLYCBASE: a revised database of O-glycosylated proteins. Nucleic Acids Research 24(1): 248-252 (1996)
1995
3		Pierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh: Periodic Sequence Patterns in Human Exons. ISMB 1995: 30-38
1993
2	EE	Pierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh: Hidden Markov Models for Human Genes. NIPS 1993: 761-768
1990
1	EE	Henrik Fredholm, Henrik Bohr, Jakob Bohr, Søren Brunak, Rodney M. J. Cotterill, Benny Lautrup, Steffen B. Petersen: A Novel Approach to Prediction of the 3-Dimensional Structures. NIPS 1990: 523-529

Coauthor Index

1	Claus A. F. Andersen	[18] [20] [21] [36]
2	Troels Arvin	[43]
3	Pierre-François Baisnée	[23]
4	Pierre Baldi	[2] [3] [5] [11] [14] [16] [17] [20] [21] [23] [24] [25]
5	Hanne Bay	[22]
6	Christian Bendixen	[43]
7	Jannick Dyrløv Bendtsen	[40]
8	Hanne Birch	[12]
9	Nikolaj Blom	[10] [13] [35]
10	Henrik Bohr	[1] [33]
11	Jakob Bohr	[1] [33]
12	Peer Bork	[38]
13	Philip E. Bourne	[41]
14	Søren Buus	[31] [34] [37]
15	Robert Bywater	[19]
16	Yves Chauvin	[2] [3] [5] [11] [14] [17] [20]
17	Jens Kaae Christensen	[31]
18	Susanna Cirera	[43]
19	Carlos Cordon-Cardo	[28]
20	Rodney M. J. Cotterill	[1]
21	Tanja la Cour	[30]
22	Hans Doll	[22]
23	Jacob Engelbrecht	[2] [3] [7]
24	Anders Fausbøll	[38]
25	Paolo Frasconi	[16] [24]
26	Henrik Fredholm	[1]
27	Merete Fredholm	[43]
28	Thomas M. Frimurer	[19]
29	Nicholas Paul Gauthier	[44]
30	Garry Gippert	[33]
31	Jan Gorodkin	[8] [15] [18] [22] [43]
32	Trine Green	[43]
33	Ramneek Gupta	[12] [29] [30] [32]
34	Jan E. Hansen	[4] [6] [9] [12]
35	John-E. S. Hansen	[4]
36	Jakob Hull Havgaard	[43]
37	Jakob Hedegaard	[43]
38	Gunnar von Heijne	[7]
39	Laurie J. Heyer	[8]
40	Anette Høj	[43]
41	Henrik Hornshøj	[43]
42	Lars Juhl Jensen	[32] [38] [44]
43	Thomas Skøt Jensen	[38] [44]
44	Svava Ósk Jónsdóttir	[39]
45	Claus B. Jørgensen	[43]
46	Flemming Steen Jørgensen	[39]
47	Can Kesmir	[42]
48	Lars Kiemer	[35]
49	Steen Knudsen	[28]
50	Per Kølster	[22]
51	Andres Kreegipuu	[10] [13]
52	Anders Krogh	[2] [3] [26] [27]
53	Kasper Lamberth	[31] [34] [37]
54	Malene Erup Larsen	[44]
55	Sanne Lise Lauemøller	[31]
56	Leif Nørskov Lauritsen	[19]
57	Benny Lautrup	[1]
58	Ulrik de Lichtenberg	[38] [44]
59	Ming-Lan Lu	[28]
60	Steen Lumholdt	[43]
61	Ole Lund	[4] [6] [9] [15] [18] [31] [33] [34] [35] [37] [42]
62	Claus Lundegaard	[31] [33] [34] [37] [42]
63	Lone B. Madsen	[43]
64	Lars Nærum	[19]
65	Bente J. Nielsen	[43]
66	Henrik Nielsen	[7] [20] [40]
67	Jens O. Nielsen	[4]
68	Morten Nielsen	[31] [33] [34] [37] [42]
69	Jette Nilsson	[9]
70	Torben F. Ørntoft	[28]
71	Tracy Palmer	[40]
72	Frank Panitz	[43]
73	Anders Gorm Pedersen	[5] [11] [14] [17] [23]
74	Steffen B. Petersen	[1]
75	Thomas Nordahl Petersen	[33]
76	Gianluca Pollastri	[16] [21] [24]
77	Flemming M. Poulsen	[30]
78	Kristoffer Rapacki	[6] [9] [12] [30]
79	Milena Sawera	[43]
80	Karsten Scheibye-Knudsen	[43]
81	Karen Skriver	[30]
82	Giovanni Soda	[16] [24]
83	Bodil Søgaard	[22]
84	Dikeos Mario Soumpasis	[27]
85	Jeppe S. Spicker	[28]
86	Hans Henrik Stærfeldt	[15] [27] [32]
87	Henrik Stengaard	[43]
88	Gary D. Stormo	[8]
89	Christina Sylvester-Hvid	[34] [37]
90	Bo Thomsen	[43]
91	David Ussery	[27]
92	Rikke K. Vingborg	[43]
93	Xuefei Wang	[43]
94	Xuegang Wang	[43]
95	Rasmus Wernersson	[43] [44]
96	David Widdick	[40]
97	Friedrik Wikman	[28]
98	Christopher T. Workman	[28]
99	Peder Worning	[27] [31] [34] [37]
100	Bujie Zahn	[43]

Colors in the list of coauthors