Søren Brunak
Professor
Brunak Group
Blegdamsvej 3B
2200 København N
- 2000
A DNA structural atlas for Escherichia coli
Pedersen, A. G., Jensen, L. J., Brunak, Søren, Staerfeldt, H. H. & Ussery, D., 2000, In: Journal of Molecular Biology. 299, 4, p. 907-30 24 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2001
- Published
On the total number of genes and their length distribution in complete microbial genomes
Skovgaard, M., Jensen, Lars Juhl, Brunak, Søren, Ussery, D. & Krogh, Anders, 2001, In: Trends in Genetics. 17, 8, p. 425-8 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2002
The atlas visualisation of genome-wide information
Skovgaard, M., Jensen, L. J., Friis, C., Stærfeldt, H. H., Worning, P., Brunak, Søren & Ussery, D. W., 2002, Methods in Microbiology. Vol. 33. p. 49-63Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- 2003
Functionality of system components: conservation of protein function in protein feature space
Jensen, L. J., Ussery, D. & Brunak, Søren, 2003, In: Genome Research. 13, 11, p. 2444-9 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
Protein feature based identification of cell cycle regulated proteins in yeast
de Lichtenberg, U., Jensen, T. S., Jensen, L. J. & Brunak, Søren, 2003, In: Journal of Molecular Biology. 329, 4, p. 663-74 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2005
Comparison of computational methods for the identification of cell cycle-regulated genes
de Lichtenberg, U., Jensen, L. J., Fausbøll, A., Jensen, T. S., Bork, P. & Brunak, Søren, 2005, In: Bioinformatics. 21, 7, p. 1164-71 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
Dynamic complex formation during the yeast cell cycle
de Lichtenberg, U., Jensen, L. J., Brunak, Søren & Bork, P., 2005, In: Science (New York, N.Y.). 307, 5710, p. 724-7 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates
Jónsdóttir, S. O., Jørgensen, Flemming Steen & Brunak, Søren, 2005, In: Bioinformatics. 21, 10, p. 2145-60 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2006
Co-evolution of transcriptional and post-translational cell-cycle regulation
Jensen, L. J., Jensen, T. S., de Lichtenberg, U., Brunak, Søren & Bork, P., 2006, In: Nature Study. 443, 7111, p. 594-7 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae
Regenberg, Birgitte, Grotkjaer, T., Winther, Ole, Fausbøll, A., Akesson, M., Bro, C., Hansen, L. K., Brunak, Søren & Nielsen, Jens Bo, 2006, In: Genome Biology (Online Edition). 7, 11, p. R107Research output: Contribution to journal › Journal article › Research › peer-review
Modelling the human immune system by combining bioinformatics and systems biology approaches
Rapin, N., Kesmir, C., Frankild, S., Nielsen, M., Lundegaard, C., Brunak, Søren & Lund, O., 2006, In: Journal of Biological Physics. 32, 3-4, p. 335-53 19 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2007
Analysis of cell death inducing compounds
Spicker, J., Pedersen, H. T., Brunak, Søren & Nielsen, H. B., 2007, In: Archives of Toxicology. 81, 11, p. 803-11 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
Evolution of cell cycle control: same molecular machines, different regulation
de Lichtenberg, U., Jensen, T. S., Brunak, Søren, Bork, P. & Jensen, L. J., 2007, In: Cell Cycle. 6, 15, p. 1819-25 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Integrative analysis for finding genes and networks involved in diabetes and other complex diseases
Bergholdt, R., Størling, Z. M., Lage, K., Karlberg, E. O., Olason, P. I., Aalund, M., Nerup, J., Brunak, Søren, Workman, C. & Pociot, Flemming, 2007, In: Genome Biology (Online Edition). 8, 11, p. R253Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Locating proteins in the cell using TargetP, SignalP and related tools
Emanuelsson, O., Brunak, Søren, von Heijne, G. & Nielsen, Henrik, 2007, In: Nature Protocols (Online). 2, 4, p. 953-71 19 p.Research output: Contribution to journal › Journal article › Research › peer-review
Modeling the adaptive immune system: predictions and simulations
Lundegaard, C., Lund, O., Kesmir, C., Brunak, Søren & Nielsen, M., 2007, In: Bioinformatics (Online). 23, 24, p. 3265-75 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
Gorodkin, J., Cirera, S., Hedegaard, J., Gilchrist, M. J., Panitz, F., Jørgensen, C., Scheibye-Knudsen, K., Arvin, T., Lumholdt, S., Sawera, M., Green, T., Nielsen, B., Havgaard, J. H., Rosenkilde, C., Wang, J., Li, H., Li, R., Liu, B., Hu, S., Dong, W. & 16 others, , 2007, In: Genome Biology. 8, R45, p. R45 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
Panitz, F., Stengaard, H., Hornshøj, H., Gorodkin, J., Hedegaard, J., Cirera, S., Thomsen, B. S., Madsen, L. B., Høj, A., Vingborg, R., Zahn, B., Wang, X., Wang, X., Wernersson, R., Jørgensen, C. B., Scheibye-Knudsen, K., Arvin, T., Lumholdt, S., Sawera, M., Green, T. & 5 others, , 2007, In: Bioinformatics. 23, 13, p. i387-91 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
The implications of alternative splicing in the ENCODE protein complement
Tress, M. L., Martelli, P. L., Frankish, A., Reeves, G. A., Wesselink, J. J., Yeats, C., Olason, P. I., Albrecht, M., Hegyi, H., Giorgetti, A., Raimondo, D., Lagarde, J., Laskowski, R. A., López, G., Sadowski, M. I., Watson, J. D., Fariselli, P., Rossi, I., Nagy, A., Kai, W. & 26 others, , 2007, In: Proceedings of the National Academy of Sciences of the United States of America. 104, 13, p. 5495-500 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2008
- Published
A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes
Hansen, K. L., Hansen, N. T., Karlberg, E. O., Eklund, A. C., Roque, F. S., Donahoe, P. K., Szallasi, Z., Jensen, T. S. & Brunak, Søren, 2008, In: Proceedings of the National Academy of Science of the United States of America. 105, 52, p. 20870-5 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis
Thorsen, K., Sørensen, K., Brems-Eskildsen, A. S., Modin, C., Gaustadnes, M., Hein, A. K., Brunak, Søren, Kruhøffer, M., Laurberg, S., Borre, M. S., Wang, K., Krainer, A. R., Tørring, N., Dyrskjøt, L., Andersen, C. & Orntoft, T. F., 2008, In: Molecular & Cellular Proteomics. 7, 7, p. 1214-24 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
Analysis and prediction of gene splice sites in four Aspergillus genomes
Wang, K., Ussery, D. W. & Brunak, Søren, 2008, In: Fungal Genetics and Biology. 46 Suppl 1, p. S14-8Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Circular reasoning rather than cyclic expression
Jensen, Lars Juhl, de Lichtenberg, U., Jensen, T. S., Brunak, Søren & Bork, P., 2008, In: Genome Biology. 9, 6, p. 403Research output: Contribution to journal › Journal article › Research › peer-review
Integration of clinical chemistry, expression, and metabolite data leads to better toxicological class separation
Spicker, J., Brunak, Søren, Frederiksen, K. & Toft, H., 2008, In: Toxicological sciences : an official journal of the Society of Toxicology. 102, 2, p. 444-54 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Linear motif atlas for phosphorylation-dependent signaling
Miller, M. L., Jensen, L. J., Diella, F., Jørgensen, C., Tinti, M., Li, L., Hsiung, M., Parker, S. A., Bordeaux, J., Sicheritz-Ponten, T., Olhovsky, M., Pasculescu, A., Alexander, J., Knapp, S., Blom, N., Bork, P., Li, S., Cesareni, G., Pawson, T., Turk, B. E. & 3 others, , 2008, In: Science Signaling. 1, 35, p. ra2Research output: Contribution to journal › Journal article › Research › peer-review
Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008)
Aebersold, R., Auffray, C., Baney, E., Barillot, E., Brazma, A., Brett, C., Brunak, S., Butte, A., Califano, A., Celis, J., Cufer, T., Ferrell, J., Galas, D., Gallahan, D., Gatenby, R., Goldbeter, A., Hace, N., Henney, A., Hood, L., Iyengar, R. & 28 others, , 2008, In: Molecular Oncology. 3, 1, p. 9-17 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2009
Expression profiling of human genetic and protein interaction networks in type 1 diabetes
Brorsson, C., Lage, K., Nielsen, J. H., Brunak, Søren & Pociot, F., 2009, In: PLoS ONE. 4, 7, p. e6250Research output: Contribution to journal › Journal article › Research › peer-review
- Published
ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization
Pappalardo, F., Halling-Brown, M. D., Rapin, N., Zhang, P., Alemani, D., Emerson, A., Paci, P., Duroux, L. P., Pennisi, M., Palladini, A., Miotto, O., Churchill, D., Rossi, E., Shepherd, A. J., Moss, D. S., Castiglione, F., Bernaschi, M., Lefranc, M-P., Brunak, S., Motta, S. & 3 others, , 2009, In: Briefings in Bioinformatics. 10, 3, p. 330-40 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The type 2 diabetes associated minor allele of rs2237895 KCNQ1 associates with reduced insulin release following an oral glucose load
Holmkvist, J., Banasik, K., Andersen, G., Unoki, H., Jensen, T. S., Pisinger, C., Borch-Johnsen, K., Sandbaek, A., Lauritzen, T., Brunak, Søren, Maeda, S., Hansen, T. & Pedersen, Oluf Borbye, 2009, In: PLoS ONE. 4, 6, p. e5872Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data
Brorsson, C., Hansen, N. T., Lage, K., Bergholdt, R., Brunak, Søren, Pociot, Flemming & Diabetes Genetics Consortium, D. G. C., Feb 2009, In: Diabetes, Obesity and Metabolism Online. 11, SUPPL. 1, p. 60-6 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Analysis of gene expression profiles of microdissected cell populations indicates that testicular carcinoma in situ is an arrested gonocyte
Sonne, Si Brask, Almstrup, Kristian, Dalgaard, M., Juncker, A. S., Edsgard, D., Ruban, L., Harrison, N. J., Schwager, C., Abdollahi, A., Huber, P. E., Brunak, Søren, Gjerdrum, L. M., Moore, H. D., Andrews, P. W., Skakkebæk, Niels Erik, Rajpert-De Meyts, E. & Leffers, H., 15 Jun 2009, In: Current Cancer Research. 69, 12, p. 5241-50 10 p.Research output: Contribution to journal › Journal article › Research
- 2010
- Published
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, M. C., 2010, In: Nature. 464, 7285, p. 59-65 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results
Gauthier, N. P., Jensen, Lars Juhl, Wernersson, R., Brunak, Søren & Jensen, T. S., 2010, In: Nucleic Acids Research. 38, Database issue, p. D699-702Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Dissecting spatio-temporal protein networks driving human heart development and related disorders
Hansen, K. L., Møllgård, K., Greenway, S., Wakimoto, H., Gorham, J. M., Workman, C. T., Bendsen, E., Hansen, N. T., Rigina, O., Roque, F. S., Wiese, C., Christoffels, V. M., Roberts, A. E., Smoot, L. B., Pu, W. T., Donahoe, P. K., Tommerup, N., Brunak, S., Seidman, C. E., Seidman, J. G. & 1 others, , 2010, In: Molecular Systems Biology. 6, p. 381Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
Olsen, Jesper Velgaard, Vermeulen, M., Santamaria, A., Kumar, C., Miller, M. L., Jensen, Lars Juhl, Gnad, F., Cox, J., Jensen, T. S., Nigg, E. A., Brunak, Søren & Mann, Matthias, 2010, In: Science Signaling. 3, 104, p. ra3 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Ancient human genome sequence of an extinct Palaeo-Eskimo
Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., Bertalan, M., Nielsen, K., Gilbert, T., Wang, Y., Raghavan, M., Campos, P., Kamp, H. L. M., Wilson, A. S., Gledhill, A., Tridico, S. & 32 others, , 11 Feb 2010, In: Nature. 463, 7282, p. 757-762 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Country-specific chemical signatures of persistent environmental compounds in breast milk
Krysiak-Baltyn, K., Toppari, J., Skakkebaek, N. E., Jensen, T. S., Virtanen, H. E., Schramm, K-W., Shen, H., Vartiainen, T., Kiviranta, H., Taboureau, O., Brunak, S., Main, K. M., Krysiak-Baltyn, K., Toppari, J., Skakkebaek, N. E., Jensen, T. S., Virtanen, H. E., Schramm, K-W., Shen, H., Vartiainen, T. & 4 others, , 1 Apr 2010, In: International Journal of Andrology. 33, 2, p. 270-8 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Protein annotation in the era of personal genomics
Blicher, T., Gupta, R., Wesolowska, A., Jensen, Lars Juhl & Brunak, Søren, 1 Jun 2010, In: Current Opinion in Structural Biology. 20, 3, p. 335-41 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
OCT4 and downstream factors are expressed in human somatic urogenital epithelia and in culture of epididymal spheres
Kristensen, D. M., Nielsen, J. E., Kalisz, M., Dalgaard, M. D., Audouze, K., Larsen, M. E., Jacobsen, G. K., Horn, T., Brunak, S., Skakkebaek, N. E., Leffers, H., Kristensen, D. M., Nielsen, J. E., Kalisz, M., Dalgaard, M. D., Audouze, K. M. L., Larsen, M. E., Jacobsen, G. K., Horn, T., Brunak, S. & 2 others, , 1 Nov 2010, In: Molecular Human Reproduction. 16, 11, p. 835-45 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2011
- Published
An Aboriginal Australian genome reveals separate human dispersals into Asia
Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E., Rasmussen, S., Albrechtsen, A., Skotte, L., Lindgreen, S., Metspalu, M., Jombart, T., Kivisild, T., Zhai, W., Eriksson, A., Manica, A., Orlando, L., De La Vega, F. M., Tridico, S., Metspalu, E., Nielsen, K., Avila Arcos, M. D. C. & 38 others, , 2011, In: Science. 334, 6052, p. 94-98 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
ChemProt: a disease chemical biology database
Taboureau, O., Nielsen, S. K., Audouze, K. M. L., Weinhold, N., Edsgärd, D., Roque, F. S., Kouskoumvekaki, I., Bora, A., Curpan, R., Jensen, T. S., Brunak, Søren & Oprea, T., 2011, In: Nucleic Acids Research. 39, Database issue, p. D367-72Research output: Contribution to journal › Journal article › Research › peer-review
Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response
Li, Q., Eklund, A. C., Birkbak, N. J., Desmedt, C., Haibe-Kains, B., Sotiriou, C., Symmans, W. F., Pusztai, L., Brunak, Søren, Richardson, A. L. & Szallasi, Z. I., 2011, In: B M C Bioinformatics. 12, p. 310Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Enterotypes of the human gut microbiome: [Plus]Corrigendum [Plus]Addendum
Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., Batto, J-M., dos Santos, M. B. Q., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K. & 31 others, , 2011, In: Nature. 473, 7346, p. 174-180 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Huntingtin-interacting protein 14 is a type 1 diabetes candidate protein regulating insulin secretion and beta-cell apoptosis
Berchtold, L. A., Størling, Z. M., Ortis, F., Lage, K., Bang-Berthelsen, C., Bergholdt, R., Hald, J., Brorsson, C. A., Eizirik, D. L., Pociot, Flemming, Brunak, Søren & Størling, Joachim, 2011, In: PNAS Early Edition. 108, 37, p. E681-8Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Intrauterine exposure to mild analgesics is a risk factor for development of male reproductive disorders in human and rat
Kristensen, D. M., Hass, U., Lesné, L., Lottrup, G., Jacobsen, P. R., Desdoits-Lethimonier, C., Boberg, J., Petersen, Jørgen Holm, Toppari, J., Jensen, T. K., Brunak, Søren, Skakkebæk, Niels Erik, Nellemann, C., Main, Katharina Maria, Jégou, B. & Leffers, H., 2011, In: Human Reproduction. 26, 1, p. 235-44 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Protein interaction-based genome-wide analysis of incident coronary heart disease
Jensen, Majken Karoline, Pers, Tune H, Dworzynski, P., Girman, C. J., Brunak, Søren & Rimm, E. B., 2011, In: Circulation: Cardiovascular Genetics. 4, 5, p. 549-56 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
SignalP 4.0: discriminating signal peptides from transmembrane regions
Petersen, T. N., Brunak, Søren, von Heijne, G. & Nielsen, H., 2011, In: Nature Methods. 8, 10, p. 785-6 2 p.Research output: Contribution to journal › Journal article › Research › peer-review
The strength of intron donor splice sites in human genes displays a bell-shaped pattern
Wang, K., Wernersson, R. & Brunak, Søren, 2011, In: Bioinformatics (Online). 27, 22, p. 3079-84 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Using electronic patient records to discover disease correlations and stratify patient cohorts
Roque, F. S., Jensen, P. B., Schmock, H., Dalgaard, M., Andreatta, M., Hansen, T., Søeby, K., Bredkjær, S., Juul, Anders, Werge, Thomas, Jensen, Lars Juhl & Brunak, Søren, 2011, In: P L o S Computational Biology. 7, 8, p. e1002141 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Bioinformatics-driven identification and examination of candidate genes for non-alcoholic fatty liver disease
Banasik, Karina, Justesen, Johanne Marie, Hornbak, M., Krarup, N. T., Gjesing, A. P., Sandholt, C. H., Søndergaard Jensen, T., Grarup, Niels, Andersson, Åsa, Jørgensen, T., Witte, D. R., Sandbæk, A., Lauritzen, T., Thorens, B., Brunak, Søren, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye & Hansen, Torben, 1 Jan 2011, In: P L o S One. 6, 1, p. e16542Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Many putative endocrine disruptors inhibit prostaglandin synthesis
Kristensen, D. M., Skalkam, M. L., Audouze, K. M. L., Lesné, L., Desdoits-Lethimonier, C., Frederiksen, H., Brunak, Søren, Skakkebæk, Niels Erik, Jégou, B., Hansen, Jacob B., Junker, S. & Leffers, H., 1 Apr 2011, In: Environmental Health Perspectives. 119, 4, p. 534-41 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes
Pers, T. H., Hansen, N. T., Hansen, K. L., Koefoed, P., Dworzynski, P., Miller, M. L., Flint, T. J., Mellerup, E., Dam, H., Andreassen, O. A., Djurovic, S., Melle, I., Børglum, A. D., Werge, T., Purcell, S., Ferreira, M. A., Kouskoumvekaki, I., Workman, C., Hansen, T., Mors, O. & 1 others, , 11 Apr 2011, In: Genetic Epidemiology. 35, 5, p. 318-332 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia
Wesolowska, A., Gautier, L., Weinhold, N., Audouze, K. M. L., Brunak, Søren, Sicheritz-Ponten, T., Gupta, R., Dalgaard, M. D., Nielsen, B. F., Leffers, H., Borst, L., Helt, L. R., Nersting, J., Schmiegelow, Kjeld, Bak, M. & Tommerup, Niels, 1 Jun 2011, In: Leukemia. 25, 6, p. 1001-1006 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A systematic study of site-specific GalNAc-type O-glycosylation modulating proprotein convertase processing
Schjoldager, Katrine Ter-Borch Gram, Vester-Christensen, M. B., Goth, C. K., Petersen, T. N., Brunak, Søren, Bennett, Eric Paul, Levery, S. B. & Clausen, Henrik, 18 Nov 2011, In: Journal of Biological Chemistry. 286, 46, p. 40122-32 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2012
- Published
A genome-wide association study of men with symptoms of testicular dysgenesis syndrome and its network biology interpretation
Dalgaard, M. D., Weinhold, N., Edsgärd, D., Silver, J. D., Pers, T. H., Nielsen, J. E., Jørgensen, N., Juul, A., Gerds, T. A., Giwercman, A., Giwercman, Y. L., Cohn-Cedermark, G., Virtanen, H. E., Toppari, J., Daugaard, G., Jensen, T. S., Brunak, S., Rajpert-De Meyts, E., Skakkebæk, N. E., Leffers, H. & 1 others, , 2012, In: Journal of Medical Genetics. 49, 1, p. 58-65 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Association between chemical pattern in breast milk and congenital cryptorchidism: modelling of complex human exposures
Krysiak-Baltyn, K., Toppari, J., Skakkebæk, Niels Erik, Jensen, T. S., Virtanen, H. E., Schramm, K., Shen, H., Vartiainen, T., Kiviranta, H., Taboureau, O., Audouze, K. M. L., Brunak, Søren & Main, Katharina Maria, 2012, In: International Journal of Andrology. 35, 3, p. 294-302 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Cometin is a novel neurotrophic factor that promotes neurite outgrowth and neuroblast migration in vitro and supports survival of spiral ganglion neurons in vivo
Jørgensen, J. R., Fransson, A., Fjord-Larsen, L., Thompson, L. H., Houchins, J. P., Andrade, N., Torp, M., Kalkkinen, N., Andersson, E., Lindvall, O., Ulfendahl, M., Brunak, Søren, Johansen, T. E. & Wahlberg, L. U., 2012, In: Experimental Neurology. 233, 1, p. 172-81 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development
Hansen, K. L., Greenway, S. C., Rosenfeld, J. A., Wakimoto, H., Gorham, J. M., Segrè, A. V., Roberts, A. E., Smoot, L. B., Pu, W. T., C Pereira, A., Mesquita, S. M., Tommerup, Niels, Brunak, Søren, Ballif, B. C., Shaffer, L. G., Donahoe, P. K., Daly, M. J., Seidman, J. G., Seidman, C. E. & Larsen, Lars Allan, 2012, In: Proceedings of the National Academy of Sciences USA (PNAS). 109, 35, p. 14035-40 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Mining electronic health records: towards better research applications and clinical care
Jensen, P. B., Jensen, Lars Juhl & Brunak, Søren, 2012, In: Nature Reviews. Genetics. 13, 6, p. 395-405 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Prediction of pH-dependent aqueous solubility of druglike molecules
Hansen, N. T., Kouskoumvekaki, I., Jørgensen, Flemming Steen, Brunak, Søren & Jónsdóttir, S. O., 2012, In: Journal of Chemical Information and Modeling. 46, 6, p. 2601-2609 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
The cancer exome generated by alternative mRNA splicing dilutes predicted HLA class I epitope density
Stranzl, T., Larsen, M. V., Lund, O., Nielsen, M. & Brunak, Søren, 2012, In: PloS one. 7, 9, p. e38670Research output: Contribution to journal › Journal article › Research › peer-review
Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology
Rojas, A. M., Santamaria, A., Malik, R., Jensen, T. S., Körner, R., Morilla, I., de Juan, D., Krallinger, M., Hansen, D. A., Hoffmann, R., Lees, J., Reid, A., Yeats, C., Wehner, A., Elowe, S., Clegg, A. B., Brunak, S., Nigg, E. A., Orengo, C., Valencia, A. & 1 others, , 2012, In: P L o S One. 7, 3, p. e31813Research output: Contribution to journal › Journal article › Research › peer-review
- Published
hERG classification model based on a combination of support vector machine method and GRIND descriptors
Li, Q., Jørgensen, Flemming Steen, Oprea, T., Brunak, Søren & Taboureau, O., 2012, In: Molecular Pharmaceutics. 5, 1, p. 117-127 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Knowledge engineering for health: a new discipline required to bridge the "ICT gap" between research and healthcare
Beck, T., Gollapudi, S., Brunak, Søren, Graf, N., Lemke, H. U., Dash, D., Buchan, I., Díaz, C., Sanz, F. & Brookes, A. J., May 2012, In: Human Mutation. 33, 5, p. 797-802 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2013
Complete genes may pass from food to human blood
Spisák, S., Solymosi, N., Ittzés, P., Bodor, A., Kondor, D., Vattay, G., Barták, B. K., Sipos, F., Galamb, O., Tulassay, Z., Szállási, Z., Rasmussen, Simon, Sicheritz-Ponten, T., Brunak, Søren, Molnár, B. & Csabai, I., 2013, In: PloS one. 8, 7, p. e69805Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Question Answering for Health Professionals and Laypersons
Maegaard, Bente, Hahn, U., Brunak, Søren, Schulz, S., Andersen, U. & Welter, S., 2013, MEDINFO 2013. Lehmann et al., C. U. (ed.). København: IMIA and IOS PressResearch output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review
- Published
The SH2 domain interaction landscape
Tinti, M., Kiemer, L., Costa, S., Miller, M. L., Sacco, F., Olsen, Jesper Velgaard, Carducci, M., Paoluzi, S., Langone, F., Workman, C., Blom, N., Machida, K., Thompson, C. M., Schutkowski, M., Brunak, Søren, Mann, Matthias, Mayer, B. J., Castagnoli, L. & Cesareni, G., 2013, In: Cell Reports. 3, 4, p. 1293-1305 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
ChemProt-2.0: visual navigation in a disease chemical biology database
Kim Kjærulff, S., Wich, L., Kringelum, J., Jacobsen, U. P., Kouskoumvekaki, I., Audouze, K., Lund, O., Brunak, Søren, Oprea, T. I. & Taboureau, O., Jan 2013, In: Nucleic Acids Research. 41, Database issue, p. D464-9Research output: Contribution to journal › Journal article › Research
- Published
Reply to 'Mining electronic health records: An additional perspective'
Jensen, P. B., Jensen, Lars Juhl & Brunak, Søren, 1 Jan 2013, In: Nature Reviews. Genetics. 14, 1 p.Research output: Contribution to journal › Comment/debate › Research › peer-review
- Published
Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology
Steentoft, C., Vakhrushev, Sergey, Joshi, Hiren Jitendra, Kong, Y., Vester-Christensen, M. B., Schjoldager, Katrine Ter-Borch Gram, Lavrsen, K., Dabelsteen, Sally, Pedersen, N. B., da Silva, L. P. M., Gupta, R., Bennett, Eric Paul, Mandel, Ulla, Brunak, Søren, Wandall, Hans H., Levery, S. B. & Clausen, Henrik, 15 May 2013, In: E M B O Journal. 32, 10, p. 1478-1488 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text
Eriksson, R., Jensen, P. B., Pletscher-Frankild, S., Jensen, Lars Juhl & Brunak, Søren, 23 May 2013, In: JAMIA - Journal of the American Medical Informatics Association. 20, 5, p. 947-953 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Transcriptome profiling of mice testes following low dose irradiation
Belling, K. C., Nielsen, H. B., Brunak, Søren, Tanaka, M., Dalgaard, M. D., Nielsen, J. E., Almstrup, Kristian & Leffers, H., 28 May 2013, In: Reproductive Biology and Endocrinology. 11, 1, 13 p., 50.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Prediction of disease causing non-synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP
Johansen, M. B., Izarzugaza, J. M. G., Brunak, Søren, Petersen, T. N. & Gupta, R., Jul 2013, In: P L o S One. 8, 7, p. e68370Research output: Contribution to journal › Journal article › Research › peer-review
- Published
MetaRanker 2.0: a web server for prioritization of genetic variation data
Pers, T. H., Dworzynski, P., Thomas, C. E., Hansen, K. L. & Brunak, Søren, 1 Jul 2013, In: Nucleic Acids Research. 41, W1, p. W104-W108Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics
Kouskoumvekaki, I., Shublaq, N. & Brunak, Søren, 1 Aug 2013, In: Briefings in Bioinformatics. 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Concordance of gene expression in human protein complexes reveals tissue specificity and pathology
Börnigen, D., Pers, T. H., Thorrez, L., Huttenhower, C., Moreau, Y. & Brunak, Søren, 5 Aug 2013, In: Nucleic Acids Research. 41, 18, p. e171Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A computational approach to chemical etiologies of diabetes
Audouze, K. M. L., Brunak, Søren & Grandjean, P., 19 Sep 2013, In: Scientific Reports. 3, p. 2712 2712.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A nondegenerate code of deleterious variants in mendelian Loci contributes to complex disease risk
Blair, D. R., Lyttle, C. S., Mortensen, J. M., Bearden, C. F., Jensen, A. B., Khiabanian, H., Melamed, R., Rabadan, R., Bernstam, E. V., Brunak, Søren, Jensen, Lars Juhl, Nicolae, D., Shah, N. H., Grossman, R. L., Cox, N. J., White, K. P. & Rzhetsky, A., 26 Sep 2013, In: Cell. 155, 1, p. 70-80 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2014
- Published
Discovery of biomarkers for glycaemic deterioration before and after the onset of type 2 diabetes: rationale and design of the epidemiological studies within the IMI DIRECT Consortium: Diabetologia
Koivula, R., Heggie, A., Barnett, A., Cederberg, H., Hansen, T. H., Koopman, A., Ridderstråle, M., Rutters, F., Vestergaard, H., Gupta, R., Herrgård, S., Heymans, M., Perry, M., Rauh, S., Siloaho, M., Teare, H. A., Thorand, B., Bell, J., Brunak, S., Frost, G. & 13 others, , 2014, In: Diabetologia. 57, 6, p. 1-11 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Discrepancies in listed adverse drug reactions in pharmaceutical product information supplied by the regulatory authorities in Denmark and the USA
Eriksson, R., Aagaard, L., Jensen, Lars Juhl, Borisova, L., Hørlück, D., Brunak, Søren & Hansen, E. H., 2014, In: Pharmacology Research & Perspectives. 2, 3, p. 1-10 e00038.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Identification of odorant-receptor interactions by global mapping of the human odorome
Audouze, K. M. L., Tromelin, A., Le Bon, A. M., Belloir, C., Petersen, R. K., Kristiansen, Karsten, Brunak, Søren & Taboureau, O., 2014, In: PLOS ONE. 9, 4, p. e93037 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Polychlorinated dibenzo-p-dioxins, furans, and biphenyls (PCDDs/PCDFs and PCBs) in breast milk and early childhood growth and IGF1
Wohlfahrt-Veje, C., Audouze, K., Brunak, Søren, Antignac, J. P., le Bizec, B., Juul, Anders, Skakkebæk, Niels Erik & Main, Katharina Maria, 2014, In: Reproduction. 147, 4, p. 391-399 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Compass: A hybrid method for clinical and biobank data mining
Krysiak-Baltyn, K., Nordahl Petersen, T., Audouze, K. M. L., Jørgensen, N., Ängquist, Lars & Brunak, Søren, Feb 2014, In: Journal of Biomedical Informatics. 47, p. 160-170Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds
Geertz-Hansen, H. M., Blom, N., Feist, A., Brunak, Søren & Petersen, T. N., 13 Feb 2014, In: Proteins: Structure, Function, and Bioinformatics. 82, 9, p. 1819-1828 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Dose-specific adverse drug reaction identification in electronic patient records: temporal data mining in an inpatient psychiatric population
Eriksson, R., Werge, T., Jensen, Lars Juhl & Brunak, Søren, Apr 2014, In: Drug Safety. 37, 4, p. 237-47 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Erratum to: Dose-Specific Adverse Drug Reaction Identification in Electronic Patient Records: Temporal Data Mining in an Inpatient Psychiatric Population
Eriksson, R., Werge, T., Jensen, Lars Juhl & Brunak, Søren, May 2014, In: Drug Safety. 37, 5, p. 379Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics
Lundby, A., Rossin, E. J., Steffensen, A. B., Acha, M. R., Newton-Cheh, C., Pfeufer, A., Lynch, S. N., Olesen, S-P., Brunak, S., Ellinor, P. T., Jukema, J. W., Trompet, S., Ford, I., Macfarlane, P. W., Krijthe, B. P., Hofman, A., Uitterlinden, A. G., Stricker, B. H., Nathoe, H. M., Spiering, W. & 8 others, , 22 Jun 2014, In: Nature Methods. 11, 8, p. 868-874 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients
Jensen, A. B., Moseley, P. L., Oprea, T. I., Ellesøe, S. G., Eriksson, R., Schmock, H., Jensen, P. B., Jensen, Lars Juhl & Brunak, Søren, 24 Jun 2014, In: Nature Communications. 5, 10 p., 4022.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells
Re, A., Workman, C. T., Waldron, L., Quattrone, A. & Brunak, Søren, 4 Aug 2014, In: Stem Cell Research. 13, 2, p. 316-328 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Patient stratification and identification of adverse event correlations in the space of 1190 drug related adverse events
Roitmann, E., Eriksson, R. & Brunak, Søren, 11 Sep 2014, In: Frontiers in Physiology. 5, 14 p., 332.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Modules, networks and systems medicine for understanding disease and aiding diagnosis
Gustafsson, M., Nestor, C. E., Zhang, H., Barabási, A., Baranzini, S., Brunak, Søren, Chung, K. F., Federoff, H. J., Gavin, A., Meehan, R. R., Picotti, P., Pujana, M. À., Rajewsky, N., Smith, K. G., Sterk, P. J., Villoslada, P. & Benson, M., Oct 2014, In: Genome Medicine. 6, 10, p. 82Research output: Contribution to journal › Journal article › Research › peer-review
- 2015
- Published
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
Forslund, K., Hildebrand, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., Pedersen, H. K., Arumugam, M., Kristiansen, K., Yvonne Voigt, A., Vestergaard, H., Hercog, R., Igor Costea, P., Roat Kultima, J., Li, J., Jørgensen, T., Levenez, F. & 9 others, , 2015, In: Nature. 528, 7581, p. 262-266 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago
Rasmussen, S., Allentoft, M. E., Nielsen, K., Orlando, L. A. A., Sikora, M., Sjögren, K-G., Pedersen, A. G., Schubert, M., Van Dam, A., Kapel, C. M. O., Nielsen, H. B., Brunak, S., Avetisyan, P., Epimakhov, A., Khalyapin, M. V., Gnuni, A., Kriiska, A., Lasak, I., Metspalu, M., Moiseyev, V. & 11 others, , 2015, In: Cell. 163, 3, p. 571-582 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Investigation of human cancers for retrovirus by low-stringency target enrichment and high-throughput sequencing
Vinner, Lasse, Mourier, T., Friis-Nielsen, J., Gniadecki, R., Dybkaer, K., Rosenberg, J., Langhoff, J. L., Flores Santa Cruz, D., Fonager, J., Izarzugaza, J. M. G., Gupta, R., Sicheritz-Ponten, T., Brunak, Søren, Willerslev, Eske, Nielsen, L. P. & Hansen, Anders Johannes, 2015, In: Scientific Reports. 5, 13 p., 13201.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios
Besenbacher, S., Liu, S., Gonzalez-Izarzugaza, J. M., Grove, J., Belling, K. G., Bork-Jensen, J., Huang, S., Als, T. D., Li, S., Yadav, R., Rubio García, A., Lescai, F., Demontis, D., Rao, J., Ye, W., Mailund, T., Møllegaard Friborg, R., Pedersen, C. N. S., Xu, R., Sun, J. & 27 others, , 2015, In: Nature Communications. 6, 9 p., 5969.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Population genomics of bronze age Eurasia
Allentoft, M. E., Sikora, M., Sjogren, K-G., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P. D. B., Schroeder, H., Ahlstrom, T., Vinner, L., Malaspinas, A. S., Margaryan, A., Higham, T., Chivall, D., Lynnerup, N., Harvig, L. L., Baron, J., Della Casa, P., Dabrowski, P., Duffy, P. R. & 46 others, , 2015, In: Nature Genetics. 522, 7555, p. 167-172 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Individualization of treatments with drugs metabolized by CES1: combining genetics and metabolomics
Rasmussen, Henrik Berg, Bjerre, D., Linnet, Kristian, Jürgens, G., Dalhoff, Kim, Stefansson, H., Hankemeier, T., Kaddurah-Daouk, R., Taboureau, O., Brunak, Søren, Houmann, T., Jeppesen, Pia, Pagsberg, Anne Katrine, Plessen, K., Dyrborg, J., Hansen, Peter Riis, Hansen, P. E., Hughes, T., Werge, Thomas & INDICES Consortium, I. C., Apr 2015, In: Pharmacogenomics. 16, 6, p. 649-65Research output: Contribution to journal › Review › Research › peer-review
- Published
A proteomic study of the regulatory role for STAT-1 in cytokine-induced beta-cell death
Rondas, D., Gudmundsdottir, V., D'Hertog, W., Crèvecoeur, I., Waelkens, E., Brunak, Søren, Mathieu, C. & Overbergh, L., Oct 2015, In: Proteomics - Clinical Applications. 9, 9-10, p. 938–952 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Long-term risk of cardiovascular and cerebrovascular disease after removal of the colonic microbiota by colectomy: a cohort study based on the Danish National Patient Register from 1996 to 2014
Jensen, A. B., Ajslev, T. A., Brunak, Søren & Sørensen, Thorkild I.A., 15 Dec 2015, In: B M J Open. 5, 8 p., e008702.Research output: Contribution to journal › Journal article › Research › peer-review
- 2016
- Published
A genomic history of aboriginal Australia
Malaspinas, A. S., Westaway, M. C., Muller, C. E., Sousa, V. C., Lao, O., Alves, I., Bergström, A., Athanasiadis, G., Cheng, J. Y., Crawford, J. E., Heupink, T. H., Macholdt, E., Peischl, S., Rasmussen, S., Schiffels, S., Subramanian, S., Wright, J. L., Albrechtsen, A., Barbieri, C., Dupanloup, I. & 55 others, , 2016, In: Nature. 538, 7624, p. 207-214 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Identification of odorant-receptor interactions by global mapping of the human odorome
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Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
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A human gut microbial gene catalogue established by metagenomic sequencing
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