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Our software is frequently cited
in independent research papers and
published in Nature, Science, and PLoS,
as well as other high-impact journals.

Published Papers

Selected scientific papers citing our software



  • A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Marcaw (Ara macao)
    Seabury CM, Dowd SE, Seabury PM, Raudsepp T, Brightsmith DJ, et al.

    PLoS ONE 8(5): e62415. doi:10.1371/journal.pone.0062415 (2013)

  • Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage
    Mohamed F. Haroon, Shihu Hu, Ying Shi, Michael Imelfort, Jurg Keller, Philip Hugenholtz, Zhiguo Yuan & Gene W. Tyson

    Nature 500, 567–570 (2013), doi:10.1038/nature12375

  • Antitumor effect of blister beetles: An ethno-medicinal practice in Karbi community and its experimental evaluation against a murine malignant tumor model
    Akalesh Kumar Verma and Surya Bali Prasad

    Journal of Ethnopharmacology

  • Changes in Glutathione, Oxidative Stress and Mitochondrial Membrane Potential in Apoptosis Involving the Anticancer Activity of Cantharidin Isolated From Red-Headed Blister Beetles
    Akalesh Kumar Verma and Surya Bali Prasad

    Anticancer Agents in Medicinal Chemistry

  • Comprehensive Analysis of BRCA1, BRCA2 and TP53 Germline Mutation and Tumor Characterization: A Portrait of Early-Onset Breast Cancer in Brazil
    Carraro DM, Koike Folgueira MAA, Garcia Lisboa BC, Ribeiro Olivieri EH, Vitorino Krepischi AC, et al.

    PLoS ONE 8(3): e57581. doi:10.1371/journal.pone.0057581

  • De novo assembly of the pennycress (Thlaspi arvense) transcriptome provides tools for the development of a winter cover crop and biodiesel feedstock
    Kevin M. Dorn, Johnathon D. Fankhauser, Donald L. Wyse, M. David Marks

    The Plant Journal

  • De novo transcriptome profiling uncovers a drastic downregulation of photosynthesis upon nitrogen deprivation in the nonmodel green alga Botryosphaerella sudeticus
    Sun D, Zhu J, Fang L, Zhang X, Chow Y, Liu J.

    BMC Genomics 2013, 14:715 doi:10.1186/1471-2164-14-715

  • Doubly heterozygous LMNA and TTN mutations revealed by exome sequencing in a severe form of dilated cardiomyopathy
    Roberta Roncarati, Chiara Viviani Anselmi, Peter Krawitz, Giovanna Lattanzi, Yskert von Kodolitsch, Andreas Perrot, Elisa di Pasquale, Laura Papa, Paola Portararo, Marta Columbaro, Alberto Forni, Giuseppe Faggian, Gianluigi Condorelli and Peter N Robinson

    European Journal of Human Genetics , (6 March 2013) | doi:10.1038/ejhg.2013.16

  • Draft Genome Sequence of Strain CBD-635, a Methicillin-Resistant Staphylococcus aureus USA100 Isolate
    Ronan K. Carroll, Whittney N. Burda, Jill C. Roberts, Kealy K. Peak, Andrew C. Cannons, and Lindsey N. Shaw

    Genome Announcements 2013 Jul-Aug; 1(4): e00491-13.

  • Evidence for Compensatory Evolution of Ribosomal Proteins in Response to Rapid Divergence of Mitochondrial rRNA
    Barreto FS, Burton RS.

    Mol Biol Evol. 2013 Feb;30(2):310-4. doi: 10.1093/molbev/mss228

  • Focused, high accuracy 5-methylcytosine quantitation with base resolution by benchtop next-generation sequencing
    Dustin R Masser, Arthur S Berg and Willard M Freeman

    Epigenetics & Chromatin 2013, 6:33 doi:10.1186/1756-8935-6-33

  • Gene expression in the deep biosphere
    William D. Orsi, Virginia P. Edgcomb, Glenn D. Christman & Jennifer F. Biddle

    Nature (2013) doi:10.1038/nature12230

  • Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
    Mads Albertsen, Philip Hugenholtz, Adam Skarshewski, Kåre L Nielsen, Gene W Tyson and Per H Nielsen

    Nature Biotechnology 31, 533–538 (2013) doi:10.1038/nbt.2579

  • High-throughput genomics in sorghum: from wholegenome resequencing to a SNP screening array
    Bekele WA, Wieckhorst S, Friedt W, Snowdon RJ

    Plant Biotechnology Journal (2013), pp. 1–14 doi: 10.1111/pbi.12106

  • Identification of genetic markers linked to anthracnose resistance in sorghum using association analysis
    Hari D. Upadhyaya, Yi-Hong Wang, Rajan Sharma, Shivali Sharma

    Theoretical and Applied Genetics, March 2013

  • Interpretation, Stratification and Evidence for Sequence Variants Affecting mRNA Splicing in Complete Human Genome Sequences
    B.C. Shirley, E.J. Mucaki, T. Whitehead, P.I. Costea, P. Akan, P.K. Rogan

    Genomics Proteomics Bioinformatics. 2013 Mar 8. pii: S1672-0229(13)00029-6. doi: 10.1016/j.gpb.2013.01.008

  • Metabolic model for the filamentous ‘Candidatus Microthrix parvicella’ based on genomic and metagenomic analyses
    Simon Jon McIlroy, Rikke Kristiansen, Mads Albertsen, Søren Michael Karst, Simona Rossetti, Jeppe Lund Nielsen, Valter Tandoi, Robert James Seviour and Per Halkjær Nielsen

    The ISME Journal , (28 February 2013) | doi:10.1038/ismej.2013.6

  • Molecular Phylogeny and Evolution of the Proteins Encoded by Coleoid (Cuttlefish, Octopus, and Squid) Posterior Venom Glands
    Tim Ruder, Kartik Sunagar, Eivind A. B. Undheim, Syed A. Ali, Tak-Cheung Wai, Dolyce H. W. Low, Timothy N. W. Jackson, Glenn F. King, Agostinho Antunes, Bryan G. Fry

    Journal of Molecular Evolution April 2013, Volume 76, Issue 4, pp 192-204

  • Separating homeologs by phasing in the tetraploid wheat transcriptome
    Ksenia V Krasileva, Vince Buffalo, Paul Bailey, Stephen Pearce, Sarah Ayling, Facundo Tabbita, Marcelo Soria, Shichen Wang, Iwgs Consortium, Eduard Akhunov, Cristobal Uauy and Jorge Dubcovsky

    Genome Biology 2013

  • Sequence Analysis of Hepatitis C Virus From Patients With Relapse After a Sustained Virological Response: Relapse or Reinfection?
    Koji Hara et al.

    J Infect Dis. (2014) 209 (1): 38-45. doi: 10.1093/infdis/jit541

  • Somatic Mutations in H-RAS in Sporadic Pheochromocytoma and Paraganglioma Identified by Exome Sequencing
    Joakim Crona, Alberto Delgado Verdugo, Rajani Maharjan, Peter Stålberg, Dan Granberg, Per Hellman and Peyman Björklund

    The Journal of Clinical Endocrinology & Metabolism (2013) jc.2012-4257

  • Somatic Mutations, Allele Loss, and DNA Methylation of the Cub and Sushi Multiple Domains 1 (CSMD1) Gene Reveals Association with Early Age of Diagnosis in Colorectal Cancer Patients
    Shull AY, Clendenning ML, Ghoshal-Gupta S, Farrell CL, Vangapandu HV, et al.

    PLoS ONE 8(3): e58731. doi:10.1371/journal.pone.0058731

  • The Norway spruce genome sequence and conifer genome evolution
    Björn Nystedt, Nathaniel R. Street, Anna Wetterbom, Andrea Zuccolo, Yao-Cheng Lin, Douglas G. Scofield, et al.

    Nature (2013)

  • TLR and IMD signaling pathways from Caligus rogercresseyi (Crustacea: Copepoda): In silico gene expression and SNPs discovery
    V. Valenzuela-Muñoz, C. Gallardo-Escárate

    Fish & Shellfish Immunology 36 (2014) 428e434

  • Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola
    Jun-Jun Liu, Rona N Sturrock and Ross Benton

    BMC Genomics 2013, 14:884 doi:10.1186/1471-2164-14-884





Selected books citing our software


  • Epigenetics in Male Reproduction: A Practical Introduction to the Informatics of Next Generation Sequencing
    Adrian E. Platts, Claudia Lalancette and Stephen A. Krawetz

    Epigenetics and Human Health

  • Next Generation Sequencing and Whole Genome Selection in Aquaculture
    Zhanjiang (John) Liu


Papers Authored By Our Experts

Selected papers




  • Alpharetroviral self-inactivating vectors: long-term transgene expression in murine hematopoietic cells and low genotoxicity
    Suerth JD, Maetzig T, Brugman MH, Heinz N, Appelt JU, Kaufmann KB, Schmidt M, Grez M, Modlich U, Baum C, Schambach A.

    Mol Ther. 2012 May;20(5):1022-32. doi: 10.1038/mt.2011.309

  • Approaches towards DNA vaccination against a skin ciliate parasite in fish
    von Gersdorff Jørgensen L, Sigh J, Kania PW, Holten-Andersen L, Buchmann K, Clark T, Rasmussen JS, Einer-Jensen K, Lorenzen N.

    PLoS One. 2012;7(11):e48129. doi: 10.1371/journal.pone.0048129

  • Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling
    Simonsen M, Maetschke SR, Ragan MA.

    Bioinformatics. 2012 Mar 15;28(6):851-7. doi: 10.1093/bioinformatics/btr720

  • Bioinformatical Clonality Analysis of Next Generation Sequencing Derived Viral Vector Integration Sites
    Arens A, Appelt JU, et al.

    Hum Gene Ther Methods. 2012 Jun 29.

  • Comparative clonal analysis of reconstitution kinetics after transplantation of hematopoietic stem cells gene marked with a lentiviral SIN or a γ-retroviral LTR vector
    Cornils K, Bartholomae CC, Thielecke L, Lange C, Arens A, et al.

    Exp Hematol. 2012 Sep 16. pii: S0301-472X(12)00384-0. doi: 10.1016/j.exphem.2012.09.003

  • European freshwater VHSV genotype Ia isolates divide into two distinct subpopulations
    Kahns S, Skall HF, Kaas RS, Korsholm H, Bang Jensen B, Jonstrup SP, Dodge MJ, Einer-Jensen K, Stone D, Olesen NJ.

    Dis Aquat Organ. 2012 May 15;99(1):23-35. doi: 10.3354/dao02444

  • First draft genome sequence of the Japanese eel, Anguilla japonica
    Henkel CV, Dirks RP, de Wijze DL, Minegishi Y, Aoyama J, Jansen HJ, Turner B, Knudsen B, Bundgaard M, Hvam KL, Boetzer M, Pirovano W, Weltzien FA, Dufour S, Tsukamoto K, Spaink HP, van den Thillart GE

    Gene. 2012 Dec 15;511(2):195-201. doi: 10.1016/j.gene.2012.09.064. Epub 2012 Sep 29.

  • Flexible P-type ATPases interacting with the membrane
    Thøgersen, L.; Nissen, P.

    Curr. Opinion in Struct. Biol. 22, 491-499 (2012)

  • Gene Ontology-driven inference of protein-protein interactions using inducers
    Maetschke SR, Simonsen M, Davis MJ, Ragan MA

    Bioinformatics. 2012 Jan 1;28(1):69-75. doi: 10.1093/bioinformatics/btr610

  • Integration frequency and intermolecular recombination of rAAV vectors in non-human primate skeletal muscle and liver
    Nowrouzi A, Penaud-Budloo M, Kaeppel C, Appelt U, Le Guiner C, Moullier P, von Kalle C, Snyder RO, Schmidt M.

    Mol Ther. 2012 Jun;20(6):1177-86. doi: 10.1038/mt.2012.47

  • Inter-species transmission of viral haemorrhagic septicaemia virus (VHSV) from turbot (Scophthalmus maximus) to rainbow trout (Onchorhynchus mykiss)
    Schönherz AA, Lorenzen N, Einer-Jensen K.

    J Gen Virol. 2012 Dec 12. [Epub ahead of print]

  • Modeling the Self-Assembly and Stability of DHPC Micelles Using Atomic Resolution and Coarse Grained MD Simulations
    Kraft, J. F.; Vestergaard, M.; Schiøtt, B.; Thøgersen, L.

    J. Chem. Theory and Comput. 8, 1556-1569 (2012)

  • Oral transmission as a route of infection for viral haemorrhagic septicaemia virus in rainbow trout, Oncorhynchus mykiss (Walbaum)
    Schönherz AA, Hansen MH, Jørgensen HB, Berg P, Lorenzen N, Einer-Jensen K.

    J Fish Dis. 2012 Jun;35(6):395-406. doi: 10.1111/j.1365-2761.2012.01358.x

  • PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data
    Sükösd Z, Knudsen B, Kjems J, Pedersen CN

    Bioinformatics. 2012 Oct 15;28(20):2691-2. doi: 10.1093/bioinformatics/bts488

  • The tomato genome sequence provides insights into fleshy fruit evolution
    The Tomato Genome Consortium

    Nature 485, 635–641 (2012) doi:10.1038/nature11119

  • Tracing Cytoplasmic Ca2+ Ion and Water Access Points in the Ca2+-ATPase
  • Typing of viral hemorrhagic septicemia virus by monoclonal antibodies
    Ito T, Kurita J, Sano M, Skall HF, Lorenzen N, Einer-Jensen K, Olesen NJ.

    J Gen Virol. 2012 Dec;93(Pt 12):2546-57. doi: 10.1099/vir.0.043091-0

  • Water-in-oil micro-emulsion enhances the secondary structure of a protein by confinement
    Shipovskov S, Oliveira CL, Hoffmann SV, Schauser L, Sutherland DS, Besenbacher F, Pedersen JS

    Chemphyschem. 2012 Sep 17;13(13):3179-84. doi: 10.1002/cphc.201200295


  • An unbiased genome-wide analysis of zinc-finger nuclease specificity
    Gabriel R, Lombardo A, Arens A, et al.

    Nat Biotechnol. 2011 Aug 7;29(9):816-23. doi: 10.1038/nbt.1948

  • Clonal inventory screens uncover monoclonality following serial transplantation of MGMT P140K-transduced stem cells and dose-intense chemotherapy
    Giordano FA, Sorg UR, Appelt JU, Lachmann N, Bleier S, Roeder I, Kleff V, Flasshove M, Zeller WJ, Allgayer H, von Kalle C, Fruehauf S, Moritz T, Laufs S.

    Hum Gene Ther. 2011 Jun;22(6):697-710

  • Distinct types of tumor-initiating cells form human colon cancer tumors and metastases
    Dieter SM, Ball CR, Hoffmann CM, Nowrouzi A, Herbst F, Zavidij O, Abel U, Arens A, Weichert W, Brand K, Koch M, Weitz J, Schmidt M, von Kalle C, Glimm H.

    Cell Stem Cell. 2011 Oct 4;9(4):357-65. doi: 10.1016/j.stem.2011.08.010

  • GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution
    Simonsen M, Thomsen R, Christensen MH, Pedersen CNS

    GECCO 2011 conference

  • GPU-accelerated high-accuracy molecular docking using guided differential evolution: real world applications
    Simonsen M, Pedersen CNS, Christensen MH, and Thomsen R

    GECCO '11 Proceedings of the 13th annual conference on Genetic and evolutionary computation Pages 1803-1810; doi>10.1145/2001576.2001818

  • Hepatocyte-targeted expression by integrase-defective lentiviral vectors induces antigen-specific tolerance in mice with low genotoxic risk
    Mátrai J, Cantore A, Bartholomae CC, Annoni A, Wang W, Acosta-Sanchez A, Samara-Kuko E, De Waele L, Ma L, Genovese P, Damo M, Arens A, Goudy K, Nichols TC, von Kalle C, L Chuah MK, Roncarolo MG, Schmidt M, Vandendriessche T, Naldini L.

    Hepatology. 2011 May;53(5):1696-707. doi: 10.1002/hep.24230

  • Inference of Large Phylogenies Using Neighbour-Joining
    Simonsen M, Mailund T, Pedersen CNS

    Communications in Computer and Information Science Volume 127, 2011, pp 334-344

  • Insertion Sites in Engrafted Cells Cluster Within a Limited Repertoire of Genomic Areas After Gammaretroviral Vector Gene Therapy
    Deichmann A, Brugman MH, Bartholomae CC, Schwarzwaelder K, Verstegen MM, Howe SJ, Arens A, Ott MG, Hoelzer D, et al.

    Mol Ther. 2011 Nov;19(11):2031-9. doi: 10.1038/mt.2011.178

  • Lentiviral vector integration profiles differ in rodent postmitotic tissues
    Bartholomae CC, Arens A, Balaggan KS, Yáñez-Muñoz RJ, Montini E, Howe SJ, Paruzynski A, Korn B, Appelt JU, Macneil A, Cesana D, Abel U, Glimm H, Naldini L, Ali RR, Thrasher AJ, von Kalle C, Schmidt M.

    Mol Ther. 2011 Apr;19(4):703-10

  • Molecular Docking with Ligand Attached Water
    Lie MA, Thomsen R, Pedersen CNS, Schiøtt B, Christensen MH

    J. Chem. Inf. Model., 2011, 51 (4), pp 909–917 DOI: 10.1021/ci100510m

  • Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars
    Sükösd Z, Knudsen B, Vaerum M, Kjems J, Andersen ES

    BMC Bioinformatics. 2011 Apr 18;12:103

  • Mutual adaptation of a membrane protein and its lipid bilayer during conformational changes
    Sonntag, Y.; Musgaard, M.; Olesen, C.; Schiøtt, B.; Møller, J. V.; Nissen, P.; Thøgersen, L.

    Nature Comm. 2, 304 (2011)

  • Protonation States of Important Acidic Residues in the Central Ca2+ Ion Binding Sites of the Ca2+-ATPase: A Molecular Modeling Study
    Musgaard, M.; Thøgersen, L.; Schiøtt, B.

    Biochemistry 50, 11109-11120 (2011)

  • Rapid computation of distance estimators from nucleotide and amino acid alignments
    Simonsen M, Pedersen CNS

    SAC '11 Proceedings of the 2011 ACM Symposium on Applied Computing Pages 89-93 ; doi>10.1145/1982185.1982208

  • Retroviral Gene Therapy for X-linked Chronic Granulomatous Disease: Results From Phase I/II Trial
    Kang HJ, Bartholomae CC, Paruzynski A, Arens A, et al.

    Mol Ther. 2011 Nov;19(11):2092-101. doi: 10.1038/mt.2011.166

  • Stable Human FIX Expression After 0.9G Intrauterine Gene Transfer of Self-complementary Adeno-associated Viral Vector 5 and 8 in Macaques
    Mattar CN, Nathwani AC, Waddington SN, Dighe N, Kaeppel C, Nowrouzi A, Mcintosh J, Johana NB, Ogden B, Fisk NM, Davidoff AM, David A, Peebles D, Valentine MB, Appelt JU, von Kalle C, Schmidt M, Biswas A, Choolani M, Chan JK.

    Mol Ther. 2011 Nov;19(11):1950-60. doi: 10.1038/mt.2011.107

  • The Medicago genome provides insight into the evolution of rhizobial symbioses
    Young ND, Debelle F, Oldroyd GED, et al.

    Nature 480, 520–524 (22 December 2011), doi:10.1038/nature10625


  • A Computer Simulator for Assessing the Different Challenges and Strategies of De Novo Sequence Assembly
    Bjarne Knudsen, Roald Forsberg and Michael M. Miyamoto

    Genes - Special Issue Next Generation DNA Sequencing

  • Analysis of self-inactivating lentiviral vector integration sites and flanking gene expression in human peripheral blood progenitor cells after alkylator chemotherapy
    Grund N, Maier P, Giordano FA, Appelt JU, Zucknick M, Li L, Wenz F, Zeller WJ, Fruehauf S, Allgayer H, Laufs S.

    Hum Gene Ther. 2010 Aug;21(8):943-56

  • Expression pattern suggests a role of MiR399 in the regulation of the cellular response to local Pi increase during arbuscular mycorrhizal symbiosis
    Branscheid A, Sieh D, Pant BD, May P, Devers EA, Elkrog A, Schauser L, Scheible WR, Krajinski F

    Mol Plant Microbe Interact. 2010 Jul;23(7):915-26. doi: 10.1094/MPMI-23-7-0915

  • Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing
    Paruzynski A, Arens A, Gabriel R, Bartholomae CC, Scholz S, Wang W, Wolf S, Glimm H, Schmidt M, von Kalle C.

    Nat Protoc. 2010 Aug;5(8):1379-95

  • QuantProReloaded: Quantitative Analysis of Microspot Immunoassays
    Anika Joecker, Johanna Sonntag, Frauke Henjes, Frank Goetschel, Achim Tresch, Tim Beissbarth, Stefan Wiemann, and Ulrike Korf

    Bioinformatics 2010, doi:10.1093/bioinformatics/btq443

  • Sparse Learner Boosting for Gene Expression Data
    Mari Pritchard

    IPSJ Transactions on Bioinformatics Vol. 3 (2010) pp. 54-61

  • Structure of nanoscale truncated octahedral DNA cages: variation of single-stranded linker regions and influence on assembly yields
    Oliveira CL, Juul S, Jørgensen HL, Knudsen B, Tordrup D, Oteri F, Falconi M, Koch J, Desideri A, Pedersen JS, Andersen FF, Knudsen BR

    ACS Nano. 2010 Mar 23;4(3):1367-76.PMID: 20146442


  • A Snapshot of the Emerging Tomato Genome Sequence
    Mueller LA, Lankhorst RK, Tanksley SD, et al.

    Plant Gen. 2009 2: 78–92 10.3835/plantgenome2008.08.0005

  • Accurate and fast methods to estimate the population mutation rate from error prone sequences
    Knudsen B, Miyamoto MM

    BMC Bioinformatics 11;10:247.PMID: 19671163

  • An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes
    Bertioli DJ, Moretzsohn MC, Madsen LH, Sandal N, Leal-Bertioli SC, Guimarães PM, Hougaard BK, Fredslund J, Schauser L, Nielsen AM, Sato S, Tabata S, Cannon SB, Stougaard J

    BMC Genomics. 2009 Jan 23;10:45. doi: 10.1186/1471-2164-10-45

  • Cold spots in hot spots: transcription start sites of active genes are spared from HIV vector integration
    Giordano FA, Appelt JU, Zucknick M, Abba M, Zeller WJ, Fruehauf S, Allgayer H, Laufs S.

    AIDS. 2009 Nov 27;23(18):2535-7

  • Comprehensive genomic access to vector integration in clinical gene therapy
    Gabriel R, Eckenberg R, Paruzynski A, Bartholomae CC, Nowrouzi A, Arens A, et al.

    Nat Med. 2009 Dec;15(12):1431-6

  • Dissection of symbiosis and organ development by integrated transcriptome analysis of lotus japonicus mutant and wild-type plants
    Høgslund N, Radutoiu S, Krusell L, Voroshilova V, Hannah MA, Goffard N, Sanchez DH, Lippold F, Ott T, Sato S, Tabata S, Liboriussen P, Lohmann GV, Schauser L, Weiller GF, Udvardi MK, Stougaard J

    PLoS One. 2009 Aug 7;4(8):e6556. doi: 10.1371/journal.pone.0006556

  • Incorporation of Antimicrobial Peptides into Membranes: A Combined Liquid-State NMR and Molecular Dynamics Study of Alamethicin in DMPC/DHPC Bicelles
    Dittmer, J.; Thøgersen, L.; Underhaug, J.; Bertelsen, K.; Vosegaard, T.; Pedersen, J. M.; Schiøtt, B.; Tajkhorshid, E.; Skrydstrup, T.; Nielsen, N. C.

    J. Phys. Chem. B 113, 6928-6937 (2009)

  • PEP1 regulates perennial flowering in Arabis alpina
    Renhou Wang, Sara Farrona, Coral Vincent, Anika Joecker, Heiko Schoof, Franziska Turck, Carlos Alonso-Blanco, George Coupland & Maria C. Albani

    Nature 459, 423-427 (21 May 2009) | doi:10.1038/nature07988

  • Prediction of the benefit of trastuzumab (T)-based therapy by the change of gene expression of peripheral blood mononuclear cells (PBMC)
    C. Shimizu, K. Tamura, F. Koizumi, O. Komori, M. Pritchard, M. H. Mollah, S. Eguchi and Y. Fujiwara

    Journal of Clinical Oncology, 2009, Vol 27, No 15S (May 20 Supplement), 2009: e14578

  • QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis
    Appelt JU, Giordano FA, Ecker M, Roeder I, Grund N, Hotz-Wagenblatt A, Opelz G, Zeller WJ, Allgayer H, Fruehauf S, Laufs S.

    Gene Ther. 2009 Jul;16(7):885-93

  • Residue-Specific Information about the Dynamics of Antimicrobial Peptides from 1H−15N and 2H Solid-State NMR Spectroscopy
    Bertelsen, K.; Paaske, B.; Thøgersen, L.; Tajkhorshid, E.; Schiøtt, B.; Skrydstrup, T.; Nielsen, N. C.; Vosegaard, T.

    J. Am. Chem. Soc. 131, 18335-18342 (2009)

  • Semiquantitative Analysis of Arabidopsis RNA by Reverse Transcription Followed by PCR Using Mimics
    I Kardailsky

    Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5297

  • Using biological networks to search for interacting loci in genome-wide association studies
    Emily M, Mailund T, Hein J, Schauser L, Schierup MH

    Eur J Hum Genet. 2009 Oct;17(10):1231-40. doi: 10.1038/ejhg.2009.15


  • Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis
    Kasper Thorsen; Karina D Sørensen; Anne Sofie Brems-Eskildsen; Charlotte Modin; Mette Gaustadnes; Anne-Mette K Hein; Mogens Kruhøffer; Søren Laurberg; Michael Borre; Kai Wang; Søren Brunak; Adrian R Krainer; Niels Tørring; Lars Dyrskjøt; Claus L Andersen & Torben F Orntoft

    Mol Cell Proteomics, Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Skejby, DK-8200 Aarhus N, Denmark., 7, 1214-1224

  • An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes
    Hougaard BK, Madsen LH, Sandal N, de Carvalho Moretzsohn M, Fredslund J, Schauser L, Nielsen AM, Rohde T, Sato S, Tabata S, Bertioli DJ, Stougaard J

    Genetics. 2008 Aug;179(4):2299-312. doi: 10.1534/genetics.108.090084

  • Assembly and structural analysis of a covalently closed nano-scale DNA cage
    Andersen FF, Knudsen B, Oliveira CL, Frøhlich RF, Krüger D, Bungert J, Agbandje-McKenna M, McKenna R, Juul S, Veigaard C, Koch J, Rubinstein JL, Guldbrandtsen B, Hede MS, Karlsson G, Andersen AH, Pedersen JS, Knudsen BR

    Nucleic Acids Res. 2008 Mar;36(4):1113-9. Epub 2007 Dec 20.

  • Effects of Selenomethionine on the Gene Expression Profile of Cloned Human Prostate Cancer Cells Representing a Phenotypic Continuum of Cancer Progression
    J. Stewart, J. Ware, C. Boysen, S. Gulati, Z. Zhou, S. Rosenfeld, L. Kopelovich and A. R. Kennedy

    Nutrition and Cancer, 60, 826-836, 2008

  • Increased cell motility and invasion upon knockdown of lipolysis stimulated lipoprotein receptor (LSR) in SW780 bladder cancer cells
    Malene Herbsleb; Karin Birkenkamp-Demtroder; Thomas Thykjaer; Carsten Wiuf; Anne-Mette K Hein; Torben F Orntoft & Lars Dyrskjøt

    BMC Med Genomics, Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Skejby, Brendstrupgaardsvej 100, DK-8200 Aarhus N, Denmark., 1, 31

  • Peptide Aggregation and Pore Formation in a Lipid Bilayer: A Combined Coarse-Grained and All Atom Molecular Dynamics Study
    Thøgersen, L.; Schiøtt, B.; Vosegaard, T.; Nielsen, N. C.; Tajkhorshid, E.

    Biophys. J. 95, 4337-4347 (2008)

  • Protein function prediction and annotation in an integrated environment powered by web services (AFAWE)
    Anika Jöcker, Fabian Hoffmann, Andreas Groscurth and Heiko Schoof

    Bioinformatics (2008) 24 (20): 2393-2394. doi: 10.1093/bioinformatics/btn394

  • Rapid Neighbour-Joining
    Simonsen M, Mailund T, Pedersen CNS

    WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics Pages 113 - 122 ; doi>10.1007/978-3-540-87361-7_10

  • Resolution Enhancement in Solid-State NMR of Oriented Membrane Proteins by Anisotropic Differential Linebroadening
    Vosegaard, T.; Bertelsen, K.; Pedersen, J. M.; Thøgersen, L.; Schiøtt, B.; Tajkhorshid, E.; Skrydstrup, T.; Nielsen, N. C.

    J. Am. Chem. Soc. 130, 5028-5029 (2008)

  • The augmented Roothaan–Hall method for optimizing Hartree–Fock and Kohn–Sham density matrices
    Høst, S.; Olsen, J.; Jansik, B.; Thøgersen, L.; Jørgensen, P.; Helgaker, T.

    J. Chem. Phys. 129, 124106 (2008)

  • The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies
    L. Shi, W. D. Jones, R. V. Jensen,, S. C. Harris, R. G. Perkins, F. M. Goodsaid, L. Guo, L. J. Croner, C. Boysen, et al.

    BMC Bioinformatics, 9, Suppl 9:S10, 2008


  • Active Signal Processing: A Counter-intuitive Approach to Enhancing Signal-to-Noise Ratio via Noise Injection
    T. George, S. Gulati, S. Menahem, J. Breaux, C.Boysen, V. Daggumati, R. Quon

    Material Research Society Proceedings: Electronic Paper 0952-F01, 2007

  • BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips
    Ernest Turro; Natalia Bochkina; Anne-Mette K Hein & Sylvia Richardson

    BMC Bioinformatics, Centre for Biostatistics, Imperial College London, UK., 8, 439

  • Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments
    Agim Ballvora, Anika Jöcker, Prisca Viehöver, Hirofumi Ishihara, Jürgen Paal, Khalid Meksem, Rémy Bruggmann, Heiko Schoof, Bernd Weisshaar and Christiane Gebhardt

    BMC Genomics 2007, 8:112 doi:10.1186/1471-2164-8-112

  • Gene Expression Signatures Predict Outcome in Non-Muscle-Invasive Bladder Carcinoma: A Multicenter Validation Study
    Dyrskjot, L.; Zieger, K.; Real, F.X.; Malats, N.; Carrato, A.; Hurst, C.; Kotwal, S.; Knowles, M.; Malmstrom, P.U.; de la Torre, M. & others

    Clinical Cancer Research, AACR, 13, 3545

  • Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
    Pel et al.

    Nat Biotechnol, 25, 221-231

  • Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
    Pel et al.

    Nat Biotechnol, DSM Food Specialties, PO Box 1, 2600 MA Delft, The Netherlands., 25, 221-231

  • Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88.
    Pel HJ, de Winde JH, Archer DB, et al.

    Nat Biotechnol. 2007 Feb;25(2):221-31. Epub 2007 Jan 28

  • Incorporating experimental design and error into coalescent/mutation models of population history
    Knudsen B, Miyamoto MM

    Genetics Aug;176(4):2335-42. Epub 2007 Jun 11.PMID: 17565962

  • Incorporating experimental design and error into coalescent/mutation models of population history
    Bjarne Knudsen & Michael M Miyamoto


  • Linear-scaling implementation of molecular response theory in self-consistent field electronic-structure theory
    Coriani, S.; Høst, S.; Jansik, B.; Thøgersen, L.; Olsen, J.; Jørgensen, P.; Reine, S.; Pawlowski, F.; Helgaker, T.; Salek, P.

    J. Chem. Phys. 126, 154108-1 - 154108-11 (2007)

  • New bioinformatic strategies to rapidly characterize retroviral integration sites of gene therapy vectors
    Giordano FA, Hotz-Wagenblatt A, Lauterborn D, Appelt JU, Fellenberg K, Nagy KZ, Zeller WJ, Suhai S, Fruehauf S, Laufs S.

    Methods Inf Med. 2007;46(5):542-7

  • Semiautomated improvement of RNA alignments
    Andersen ES, Lind-Thomsen A, Knudsen B, Kristensen SE, Havgaard JH, Torarinsson E, Larsen N, Zwieb C, Sestoft P, Kjems J, Gorodkin J.

    RNA Nov;13(11):1850-9. Epub 2007 Sep 5.

  • The conserved cysteine-rich domain of a tesmin/TSO1-like protein binds zinc in vitro and TSO1 is required for both male and female fertility in Arabidopsis thaliana
    Andersen SU, Algreen-Petersen RG, Hoedl M, Jurkiewicz A, Cvitanich C, Braunschweig U, Schauser L, Oh SA, Twell D, Jensen EØ

    J Exp Bot. 2007;58(13):3657-70


  • A general pipeline for the development of anchor markers for comparative genomics in plants
    Fredslund J, Madsen LH, Hougaard BK, Nielsen AM, Bertioli D, Sandal N, Stougaard J, Schauser L

    BMC Genomics. 2006 Aug 14;7:207

  • A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates
    Anne-Mette K Hein & Sylvia Richardson

    BMC Bioinformatics, Dept. of Epidemiology and Public Health, Imperial College London, Norfolk Place, London, UK., 7, 353

  • Evaluation of DNA microarray results with quantitative gene expression platforms
    R. Canales, Y. Luo, J. C. Willey, B. Austermiller, C. C. Barbacioru, C. Boysen, et al.

    Nature Biotechnology, 24, 1115-1122, 2006

  • GeMprospector--online design of cross-species genetic marker candidates in legumes and grasses
    Fredslund J, Madsen LH, Hougaard BK, Sandal N, Stougaard J, Bertioli D, Schauser L

    Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W670-5

  • GeneRecon--a coalescent based tool for fine-scale association mapping
    Mailund T, Schierup MH, Pedersen CN, Madsen JN, Hein J, Schauser L

    Bioinformatics. 2006 Sep 15;22(18):2317-8

  • MolDock: A New Technique for High-Accuracy Molecular Docking
    Thomsen R, Christensen MH

    J. Med. Chem. 2006

  • Neuronal transcriptome of aplysia: neuronal compartments and circuitry
    Moroz et al.

    Cell, 127, 1453-1467

  • Porcine APP cDNAs: molecular cloning and characterization, expression analysis, chromosomal localization and SNP analysis
    Marianne Abildgaard Oerum; Christian Bendixen; Lone Bruhn Madsen & Knud Larsen

    Biochim Biophys Acta, 1759, 378-384

  • Protein Functional Annotation through Phylogenomics-Based Bayesian Inference
  • Regulation of flowering in the long-day grass Lolium temulentum by gibberellins and the FLOWERING LOCUS T gene
    King RW, Moritz T, Evans LT, Martin J, Andersen CH, Blundell C, Kardailsky I, Chandler PM.

    Plant Physiol. 2006 June; 141(2): 498–507. doi: 10.1104/pp.106.076760

  • Retroviral vector insertions in T-lymphocytes used for suicide gene therapy occur in gene groups with specific molecular functions
    Giordano FA, Fehse B, Hotz-Wagenblatt A, Jonnakuty S, del Val C, Appelt JU, Nagy KZ, Kuehlcke K, Naundorf S, Zander AR, Zeller WJ, Ho AD, Fruehauf S, Laufs S.

    Bone Marrow Transplant. 2006 Aug;38(3):229-35

  • The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
    MAQC Consortium

    Nature Biotechnology, 24, 1151-1161, 2006

  • Using RNA sample titrations to assess microarray platform performance and normalization techniques
    R. Shippy, S. Fulmer-Smentek, R. V. Jensen, W. D. Jones, P. K. Wolber, C. D. Johnson, P. S. Pine, C. Boysen, et al.

    Nature Biotechnology, 24, 1123-1131, 2006


  • Activity-Based Computing: Support for Mobility and Collaboration in Ubiquitous Computing
    Bardram, Jakob E.

    Personal and Ubiquitous Computing, July 2005

  • BGX: a fully Bayesian integrated approach to the analysis of Affymetrix GeneChip data
    Anne-Mette K Hein; Sylvia Richardson; Helen C Causton; Graeme K Ambler & Peter J Green

    Biostatistics, Department of Epidemiology and Public Health, Imperial College, Norfolk Place, London W2 1PG, UK., 6, 349-373

  • CoaSim: a flexible environment for simulating genetic data under coalescent models
    Mailund T, Schierup MH, Pedersen CN, Mechlenborg PJ, Madsen JN, Schauser L

    BMC Bioinformatics. 2005 Oct 14;6:252

  • Divergence time of porcine reproductive and respiratory syndrome virus subtypes
    Roald Forsberg

    Mol Biol Evol, 22, 2131-2134

  • Evolution of NIN-like proteins in Arabidopsis, rice, and Lotus japonicus
    Schauser L, Wieloch W, Stougaard J

    J Mol Evol. 2005 Feb;60(2):229-37

  • From Desktop Task Management to Ubiquitous Activity-Based Computing
    Bardram, Jakob E.

    Victor Kaptelinin and Mary Czerwinski, editors, Integrated Digital Work Environments: Beyond the Desktop Metaphor. MIT Press, 2005

  • Genome update: prediction of membrane proteins in prokaryotic genomes
    Jannick D Bendtsen; Tim T Binnewies; Peter F Hallin & David W Ussery

    Microbiology, 151, 2119-2121

  • Genome update: prediction of membrane proteins in prokaryotic genomes
    Bendtsen JD, Binnewies TT, Hallin PF, Ussery DW.

    Microbiology. 2005 Jul;151(Pt 7):2119-21

  • Genome update: prediction of secreted proteins in 225 bacterial proteomes
    Jannick D Bendtsen; Tim T Binnewies; Peter F Hallin; Thomas Sicheritz-Pontén & David W Ussery

    Microbiology, 151, 1725-1727

  • Genome update: prediction of secreted proteins in 225 bacterial proteomes
    Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Pontén T, Ussery DW.

    Microbiology. 2005 Jun;151(Pt 6):1725-7. Review. No abstract available

  • Genome Update: Protein secretion systems in 225 bacterial genomes
    Tim T Binnewies; Jannick D Bendtsen; Peter F Hallin; Natasja Nielsen; Trudy M Wassenaar; Martin Bastian Pedersen; Per Klemm & David W Ussery

    Microbiology, 151, 1013-1016

  • Genome Update: Protein secretion systems in 225 bacterial genomes
    Binnewies TT, Bendtsen JD, Hallin PF, Nielsen N, Wassenaar TM, Pedersen MB, Klemm P, Ussery DW.

    Microbiology. 2005 Apr;151(Pt 4):1013-6. No abstract available

  • Interchromosomal segmental duplications explain the unusual structure of PRSS3, the gene for an inhibitor-resistant trypsinogen
    L.Rowen, E.Williams, G. Glusman, E. Linardopoulou, C. Friedman, M. E. Ahearn, J. Seto, C. Boysen, et al.

    Molecular Biology and Evolution 22, 1712-1720, 2005

  • LORE1, an active low-copy-number TY3-gypsy retrotransposon family in the model legume Lotus japonicus
    Madsen LH, Fukai E, Radutoiu S, Yost CK, Sandal N, Schauser L, Stougaard J

    Plant J. 2005 Nov;44(3):372-81

  • Mobility Work - The Spatial Dimension of Collaboration at a Hospital
    Bardram, Jakob E. and Bossen, Claus

    Journal of Computer Supported Cooperative Work, 14(2), p. 131-160, 2005

  • NetAcet: prediction of N-terminal acetylation sites
    Lars Kiemer; Jannick Dyrløv Bendtsen & Nikolaj Blom

    Bioinformatics, 21, 1269-1270

  • Non-classical protein secretion in bacteria
    Bendtsen JD, Kiemer L, Fausbøll A, Brunak S.

    BMC Microbiol. 2005 Oct 7;5:58

  • Prediction of twin-arginine signal peptides
    Jannick Dyrløv Bendtsen; Henrik Nielsen; David Widdick; Tracy Palmer & Søren Brunak

    BMC Bioinformatics, 6, 167

  • Prediction of twin-arginine signal peptides
    Bendtsen JD, Nielsen H, Widdick D, Palmer T, Brunak S.

    BMC Bioinformatics. 2005 Jul 2;6:167

  • PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs
    Fredslund J, Schauser L, Madsen LH, Sandal N, Stougaard J

    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W516-20

  • The Java Context Awareness Framework (JCAF) - A Service Infrastructure and Programming Framework for Context-Aware Applications
    Bardram, Jakob E.

    Hans Gellersen, Roy Want, and Albrecht Schmidt, editors, Proceedings of the 3rd International Conference on Pervasive Computing (Pervasive 2005), Lecture Notes in Computer Science, Munich, Germany, May 2005. Springer Verlag

  • The Trouble with Login - On Usability and Computer Security in Ubiquitous Computing
    Bardram, Jakob E.

    Personal and Ubiquitous Computing, 9(6), Pages 357 - 367

  • The trust-region self-consistent field method in Kohn-Sham density-functional theory
    Thøgersen, L.; Olsen, J.; Köhn, A.; Jørgensen, P.; Salek, P.; Helgaker, T.

    J. Chem. Phys. 123, 074103-1 - 074103-17 (2005)

  • Tree measures and the number of segregating sites in time-structured population samples
    Roald Forsberg; Alexei J Drummond & Jotun Hein

    BMC Genet, 6, 35

  • Using equilibrium frequencies in models of sequence evolution
    Knudsen B, Miyamoto MM

    BMC Evol Biol. Mar 2;5(1):21.PMID: 15743518

  • Using equilibrium frequencies in models of sequence evolution
    Bjarne Knudsen & Michael M Miyamoto

    BMC Evol Biol, 5, 21


  • A comparative method for finding and folding RNA secondary structures within protein-coding regions
    Jakob Skou Pedersen; Irmtraud Margret Meyer; Roald Forsberg; Peter Simmonds & Jotun Hein

    Nucleic Acids Res, 32, 4925-4936

  • A coupled cluster and full configuration interaction study of CN and CN-
    Thøgersen, L.; Olsen, J.

    Chem. Phys. Lett. 393, 36-43 (2004)

  • Acceleration of flowering by overexpression of MFT (MOTHER OF FT AND TFL1)
    Yoo SY, Kardailsky I, Lee JS, Weigel D, Ahn JH.

    Mol Cells. 2004 Feb 29;17(1):95-101

  • Activity-Based Support for Mobility and Collaboration in Ubiquitous Computing
    Bardram, Jakob E.

    Luciano Baresi, editor, Proceedings of the Second International Conference on Ubiquitous Mobile Information and Collaboration Systems, Lecture Notes in Computer Science, pages 169 - 184, Riga, Latvia, September 2004. Springer Verlag

  • An evolutionary model for protein-coding regions with conserved RNA structure
    Jakob Skou Pedersen; Roald Forsberg; Irmtraud Margret Meyer & Jotun Hein

    Mol Biol Evol, 21, 1913-1922

  • Applications of Context-Aware Computing in Hospital Work Ð Examples and Design Principles
    Bardram, Jakob E.

    Proceedings of ACM Symposium on Applied Computing (ACM SAC) 2004, pages 1574-1579. ACM Press, 2004

  • Architectural Prototyping: An Approach for Grounding Architectural Design and Learning
    Bardram, Jakob E., Christensen, Henrik B. and Hansen, Klaus M.

    Proceedings of Fourth Working IEEE/IFIP Conference on Software Architecture (WICSA'04), pages 15 - 24. IEEE Press, 2004

  • CITRX thioredoxin interacts with the tomato Cf-9 resistance protein and negatively regulates defence
    Rivas S, Rougon-Cardoso A, Smoker M, Schauser L, Yoshioka H, Jones JD

    EMBO J. 2004 May 19;23(10):2156-65

  • Development of in vitro transposon assisted signal sequence trapping and its use in screening Bacillus halodurans C125 and Sulfolobus solfataricus P2 gene libraries
    Fiona Becker; Kirk Schnorr; Reinhard Wilting; Niels Tolstrup; Jannick Dyrløv Bendtsen & Peter Bjarke Olsen

    J Microbiol Methods, 57, 123-133

  • Development of in vitro transposon assisted signal sequence trapping and its use in screening Bacillus halodurans C125 and Sulfolobus solfataricus P2 gene libraries
    Becker F, Schnorr K, Wilting R, Tolstrup N, Bendtsen JD, Olsen PB.

    J Microbiol Methods. 2004 Apr;57(1):123-33

  • Domain Theory for Concurrency
    Nygaard, M. and Winskel, G.

    Theoretical Computer Science, 316, Pages 153-190

  • Equilibrium Geometry of the Ethynyl (CCH) Radical
    Szalay, P.G.; Thøgersen, L.S.; Olsen, J.; Kállay, M.; Gauss, J.

    J. Phys. Chem. A. 108, 3030-3034 (2004)

  • Evolution of the fish rhabdovirus viral haemorrhagic septicaemia virus
    Katja Einer-Jensen; Peter Ahrens; Roald Forsberg & Niels Lorenzen

    J Gen Virol, 85, 1167-1179

  • Evolutionary divergence of thyrotropin receptor structure
    Bjarne Knudsen & Nadir R Farid

    Mol Genet Metab, 81, 322-334

  • Evolutionary rate variation and RNA secondary structure prediction
    B. Knudsen; E. S. Andersen; C. Damgaard; J. Kjems & J. Gorodkin

    Comput Biol Chem, 28, 219-226

  • Evolutionary rate variation and RNA secondary structure prediction
    B. Knudsen; E. S. Andersen; C. Damgaard; J. Kjems & J. Gorodkin

    Comput Biol Chem, 28, 219-226

  • Feature-based prediction of non-classical and leaderless protein secretion
    Jannick Dyrløv Bendtsen; Lars Juhl Jensen; Nikolaj Blom; Gunnar Von Heijne & Søren Brunak

    Protein Eng Des Sel, 17, 349-356

  • Feature-based prediction of non-classical and leaderless protein secretion
    Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S.

    Protein Eng Des Sel. 2004 Apr;17(4):349-56. Epub 2004 Apr 28

  • Improved prediction of signal peptides: SignalP 3.0
    Jannick Dyrløv Bendtsen; Henrik Nielsen; Gunnar von Heijne & Søren Brunak

    J Mol Biol, 340, 783-795

  • Improved prediction of signal peptides: SignalP 3.0
    Bendtsen JD, Nielsen H, von Heijne G, Brunak S.

    J Mol Biol. 2004 Jul 16;340(4):783-95

  • NetAcet: prediction of N-terminal acetylation sites
    Kiemer L, Bendtsen JD, Blom N.

    Bioinformatics. 2005 Apr 1;21(7):1269-70. Epub 2004 Nov 11

  • Real-time Collaboration in Activity-based Architectures
    Bardram, Jakob E. and Christensen, Henrik B.

    Proceedings of Fourth Working IEEE/IFIP Conference on Software Architecture (WICSA'04), pages 325 - 329. IEEE Press, 2004

  • RNA interactions in the 5' region of the HIV-1 genome
    Christian Kroun Damgaard; Ebbe Sloth Andersen; Bjarne Knudsen; Jan Gorodkin & Jørgen Kjems

    J Mol Biol, 336, 369-379

  • Role of the trans-activation response element in dimerization of HIV-1 RNA
    Ebbe S Andersen; Sonia Antoranz Contera; Bjarne Knudsen; Christian K Damgaard; Flemming Besenbacher & Jørgen Kjems

    J Biol Chem, 279, 22243-22249

  • The AWARE architecture: supporting context-mediated social awareness in mobile cooperation
    Bardram, Jakob E. and Hansen, Thomas R.

    Proceedings of the 2004 ACM conference on Computer supported cooperative work, pages 192 - 201. ACM Press, 2004

  • The trust-region self-consistent field method: Towards a black-box optimization in Hartree–Fock and Kohn–Sham theories
    Thøgersen, L.; Olsen, J.; Yeager, D.; Jørgensen, P.; Salek, P.; Helgaker, T.

    J. Chem. Phys. 121, 16 (2004)


  • A codon-based model of host-specific selection in parasites, with an application to the influenza A virus
    Roald Forsberg & Freddy Bugge Christiansen

    Mol Biol Evol, 20, 1252-1259

  • Context-Aware User Authentication - Supporting Proximity-Based Login in Pervasive Computing
    Bardram, J. E., Kjær, R. E. and Pedersen, M. Ø.

    A. Dey, J. McCarthy, and A. Schmidt, editors, Proceedings of Ubicomp 2003: Ubiquitous Computing, volume 2864 of Lecture Notes in Computer Science, pages 107Ð123, Seattle, Washington, USA, Oct. 2003. Springer Verlag

  • Domain Theory for Concurrency
    Nygaard, M.

    PhD Dissertation, University of Aarhus

  • Evolution of the thyrotropin receptor: a G protein coupled receptor with an intrinsic capacity to dimerize
    Kaczur et al.

    Mol Genet Metab, 78, 275-290

  • Full Abstraction for HOPLA
    Nygaard, M. and Winskel, G.

    Proceedings of CONCUR'03, LNCS 2761, Springer-Verlag

  • Inferring evolutionary rates using serially sampled sequences from several populations
    Allen G Rodrigo; Matthew Goode; Roald Forsberg; Howard A Ross & Alexei Drummond

    Mol Biol Evol, 20, 2010-2018

  • Pfold: RNA secondary structure prediction using stochastic context-free grammars
    Bjarne Knudsen & Jotun Hein

    Nucleic Acids Res, 31, 3423-3428

  • Sequence alignments and pair hidden Markov models using evolutionary history
    Bjarne Knudsen & Michael M Miyamoto

    J Mol Biol, 333, 453-460

  • SRPDB: Signal Recognition Particle Database
    Magnus Alm Rosenblad; Jan Gorodkin; Bjarne Knudsen; Christian Zwieb & Tore Samuelsson

    Nucleic Acids Res, 31, 363-364

  • Supporting local mobility in healthcare by application roaming among heterogeneous devices
    Bardram, Jakob E., Kjær, T. A. K. and Nielsen, C.

    Proceedings of the Fifth International Conference on Human Computer Interaction with Mobile Devices and Services. Springer Verlag, 2003

  • The Sym35 gene required for root nodule development in pea is an ortholog of Nin from Lotus japonicus
    Borisov AY, Madsen LH, Tsyganov VE, Umehara Y, Voroshilova VA, Batagov AO, Sandal N, Mortensen A, Schauser L, Ellis N, Tikhonovich IA, Stougaard J

    Plant Physiol. 2003 Mar;131(3):1009-17

  • tmRDB (tmRNA database)
    Christian Zwieb; Jan Gorodkin; Bjarne Knudsen; Jody Burks & Jacek Wower

    Nucleic Acids Res, 31, 446-447

  • Using evolutionary rates to investigate protein functional divergence and conservation. A case study of the carbonic anhydrases
    Bjarne Knudsen; Michael M Miyamoto; Philip J Laipis & David N Silverman

    Genetics, 164, 1261-1269


  • Genomic analysis of the olfactory receptor region of the mouse and human T-cell receptor a/d region
    R. P. Lane, J. C. Roach, I. Y. Lee, C. Boysen, A. Smit, B. J. Trask, and L. Hood

    Genome Research 12, 81-87, 2002

  • HOPLA - A Higher-Order Process Language
    Nygaard, M. and Winskel, G.

    Proceedings of CONCUR'02, LNCS 2421, Springer-Verlag

  • Linearity in Process Languages
    Nygaard, M. and Winskel, G.

    Proceedings of LICS'02, IEEE

  • Phylogenetic and functional analysis of the bacteriophage P1 single-stranded DNA-binding protein
    Jannick Dyrløv Bendtsen; Anders S Nilsson & Hansjörg Lehnherr

    J Virol, 76, 9695-9701

  • Phylogenetic and functional analysis of the bacteriophage P1 single-stranded DNA-binding protein
    Bendtsen JD, Nilsson AS, Lehnherr H.

    J Virol. 2002 Oct;76(19):9695-701

  • Stability, Metastability, and Unstability of Three-Electron-Bonded Radical Anions. A Model ab Initio Theoretical Study
    Braïda, B.; Thøgersen, L.; Wu, W.; Hiberty, P.C.

    J. Am. Chem. Soc. 124, 11781-11790 (2002)

  • Supporting Human Activities Ñ Exploring Activity-Centered Computing
    Christensen, H. B. and Bardram, J. E.

    Proceeding of Ubiquitous Computing 2002 (UBICOMP 2002), Springer LNCS 2498, Berlin, 2002

  • The genetic diversity of European type PRRSV is similar to that of the North American type but is geographically skewed within Europe
    Roald Forsberg; Torben Storgaard; Henriette S Nielsen; Martin B Oleksiewicz; Paolo Cordioli; Giovanni Sala; Jotun Hein & Anette Bøtner

    Virology, 299, 38-47

  • The missing link: augmenting biology laboratory notebooks
    Wendy E. Mackay, Guillaume Pothier, Catherine Letondal, Kaare Bøegh and Hans Erik Sørensen

    Proceedings of the 15th annual ACM symposium on User interface software and technology. ACM Press, 2002

  • Transcriptional regulation of the stem cell leukemia gene (SCL)--comparative analysis of five vertebrate SCL loci
    Berthold Göttgens; Linda M Barton; Michael A Chapman; Angus M Sinclair; Bjarne Knudsen; Darren Grafham; James G R Gilbert; Jane Rogers; David R Bentley & Anthony R Green

    Genome Res, 12, 749-759

  • Ubiquitin ligase-associated protein SGT1 is required for host and nonhost disease resistance in plants
    Peart JR, Lu R, Sadanandom A, Malcuit I, Moffett P, Brice DC, Schauser L, Jaggard DA, Xiao S, Coleman MJ, Dow M, Jones JD, Shirasu K, Baulcombe DC

    Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10865-9


  • A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames
    A. M. Pedersen & J. L. Jensen

    Mol Biol Evol, Department of Theoretical Statistics, Institute of Mathematics, University of Aarhus, Denmark., 18, 763-776

  • A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins
    B. Knudsen & M. M. Miyamoto

    Proc Natl Acad Sci U S A, 98, 14512-14517

  • A Molecular Clock Dates the Common Ancestor of European-type Porcine Reproductive and Respiratory Syndrome Virus at More Than 10 Years before the Emergence of Disease
    Forsberg, R.; Oleksiewicz, M.B.; Krabbe Petersen, A.M.; Hein, J.; Bøtner, A. & Storgaard, T.

    Virology, Elsevier, 289, 174-179

  • A molecular clock dates the common ancestor of European-type porcine reproductive and respiratory syndrome virus at more than 10 years before the emergence of disease
    R. Forsberg; M. B. Oleksiewicz; A. M. Petersen; J. Hein; A. Bøtner & T. Storgaard

    Virology, 289, 174-179

  • Comparative genomics of the human and mouse T cell receptor loci
    G. Glusman, L. Rowen, I. Lee, C. Boysen, J. C. Roach, A. F. A. Smit, K. Wang, B. F. Koop, L. Hood

    Immunity 15, 337-349, 2001

  • Genetic heterogeneity of SAT-1 type foot-and-mouth disease viruses in southern Africa
    A. D. Bastos; D. T. Haydon; R. Forsberg; N. J. Knowles; E. C. Anderson; R. G. Bengis; L. H. Nel & G. R. Thomson

    Arch Virol, 146, 1537-1551

  • Initial sequencing and analysis of the human genome
    International Human Genome Sequencing Consortium

    Nature 409, 860-921, 2001

  • Investigation of some starting protocols for BDF (FIRM) in electrochemical digital simulation
    Britz, D.; Strutwolf, J.; Thøgersen, L.

    J. Electroanal. Chem. 512, 119-123 (2001)

  • Reversion of a live porcine reproductive and respiratory syndrome virus vaccine investigated by parallel mutations
    H. S. Nielsen; M. B. Oleksiewicz; R. Forsberg; T. Stadejek; A. Bøtner & T. Storgaard

    J Gen Virol, 82, 1263-1272

  • SRPDB (Signal Recognition Particle Database)
    J. Gorodkin; B. Knudsen; C. Zwieb & T. Samuelsson

    Nucleic Acids Res, 29, 169-170

  • The inference of stepwise changes in substitution rates using serial sequence samples
    A. Drummond; R. Forsberg & A. G. Rodrigo

    Mol Biol Evol, 18, 1365-1371

  • tmRDB (tmRNA database)
    B. Knudsen; J. Wower; C. Zwieb & J. Gorodkin

    Nucleic Acids Res, 29, 171-172


  • Activation tagging in Arabidopsis
    Weigel D, Ahn JH, Blázquez MA, Borevitz JO, Christensen SK, Fankhauser C, Ferrándiz C, Kardailsky I, et al.

    Plant Physiology April 2000 vol. 122 no. 4 1003-1014 doi: http:/​/​dx.​doi.​org/​10.​1104/​pp.​122.​4.​1003

  • Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites
    Yang, Z.; Nielsen, R.; Goldman, N. & Pedersen, A.M.K.

    Genetics, Genetics Soc America, 155, 431-449

  • Physical interaction between Wilms tumor 1 and p73 proteins modulates their functions
    Scharnhorst V, Dekker P, van der Eb AJ, Jochemsen AG

    J Biol Chem. 2000 Apr 7;275(14):10202-11

  • Scenario-Based Design of Cooperative Systems - Re-designing an Hospital Information System in Denmark
    Bardram, Jakob E.

    Group Decision and Negotiation, 9: p. 237-250

  • Temporal Coordination: On Time and Coordination of Collaborative Activities at a Surgical Department
    Bardram, Jakob E.

    Journal of Computer Supported Cooperative Work, 9: p. 157-187

  • The Lotus japonicus LjSym4 gene is required for the successful symbiotic infection of root epidermal cells
    Bonfante P, Genre A, Faccio A, Martini I, Schauser L, Stougaard J, Webb J, Parniske M

    Mol Plant Microbe Interact. 2000 Oct;13(10):1109-20

  • Transformation of Medicago truncatula via infiltration of seedlings or flowering plants with Agrobacterium
    Trieu, A. T., Burleigh, S. H., Kardailsky, I. V., et al.

    The Plant Journal, 22: 531–541. doi: 10.1046/j.1365-313x.2000.00757.x


  • A plant regulator controlling development of symbiotic root nodules
    Schauser L, Roussis A, Stiller J, Stougaard J

    Nature. 1999 Nov 11;402(6758):191-5

  • Acceleration of Flowering by Overexpression of MFT
    SY Yoo, I Kardailsky, JS Lee, D Weigel, JH Ahn

    Mol. Cells 17 (1), 95-101

  • Activation tagging of the floral inducer FT
    Kardailsky I, Shukla VK, Ahn JH, Dagenais N, Christensen SK, Nguyen JT, Chory J, Harrison MJ, Weigel D.

    Science 3 December 1999: 286 (5446), 1962-1965. DOI:10.1126/science.286.5446.1962

  • Identification and characterization of the single-stranded DNA-binding protein of bacteriophage P1
    H. Lehnherr; J. D. Bendtsen; F. Preuss & T. V. Ilyina

    J Bacteriol, 181, 6463-6468

  • Identification and characterization of the single-stranded DNA-binding protein of bacteriophage P1
    Lehnherr H, Bendtsen JD, Preuss F, Ilyina TV.

    J Bacteriol. 1999 Oct;181(20):6463-8

  • Internal translation initiation generates novel WT1 protein isoforms with distinct biological properties
    Scharnhorst V, Dekker P, van der Eb AJ, Jochemsen AG

    J Biol Chem. 1999 Aug 13;274(33):23456-62

  • RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
    B. Knudsen & J. Hein

    Bioinformatics, 15, 446-454


  • A codon-based model designed to describe lentiviral evolution
    A. K. Pedersen; C. Wiuf & F. B. Christiansen

    Mol Biol Evol, Institute of Biological Sciences, University of Aarhus, Denmark., 15, 1069-1081

  • Designing for the Dynamics of Cooperative Work Activities
    Bardram, Jakob E.

    Proceedings of The 1998 ACM Conference on Computer Supported Cooperative Work, Seattle, Washington, USA. ACM Press

  • Symbiotic gene sym31 controls the presence of a lectinlike glycoprotein in the symbiosome compartment of nitrogen-fixing pea nodules
    P Dahiya, DJ Sherrier, IV Kardailsky, AY Borisov, NJ Brewin

    Molecular plant-microbe interactions 11 (9), 915-923

  • Symbiotic mutants deficient in nodule establishment identified after T-DNA transformation of Lotus japonicus
    Schauser L, Handberg K, Sandal N, Stiller J, Thykjaer T, Pajuelo E, Nielsen A, Stougaard J

    Mol Gen Genet. 1998 Sep;259(4):414-23



  • Analysis of the human T cell receptor / locus. New approaches to mapping and sequencing
    C. Boysen

    Thesis for the Ph. D. degree in biology/immunology, Division of Biology, California Institute of Technology, 1996

  • Construction and characterization of a human Bacterial Artificial Chromosome library
    U.-J. Kim, B. Birren, Y.-L. Sheng, T. Slepak, V. Mancino, C. Boysen, H.-L. Kang, M. I. Simon, and H. Shizuya

    Genomics 34, 213-218, 1996

  • Expression of cysteine protease genes in pea nodule development and senescence
    Kardailsky IV, Brewin NJ.

    Mol Plant Microbe Interact. 1996 Nov;9(8):689-95

  • Flower Development in Weeds and Trees
    Weigel, Detlef; Blazquez, Miguel; Brentt, Dana R.; Christensen, Sioux; Kardailsky, Igor; et al.

    Plant Physiology Rockville 111 (2 suppl.)

  • Identification of a new pea gene, PsNlec1, encoding a lectin-like glycoprotein isolated from the symbiosomes of root nodules
    IV Kardailsky, DJ Sherrier, NJ Brewin

    Plant Physiol. 1996 May; 111(1): 49–60

  • Identifying DNA polymorphisms in human TCRA/D variable genes by direct sequencing of PCR products
    C. Boysen, C. Carlson, E. Hood, L. E. Hood, and D. A. Nickerson

    Immunogenetics 44, 121-127, 1996

  • Localization of lipoxygenase proteins and mRNA in pea nodules: Identification of lipoxygenase in the lumen of infection threads
    CD Gardner, DJ Sherrier, IV Kardailsky, NJ Brewin

    MPMI-Molecular Plant Microbe Interactions 9 (4), 282-289

  • MDMX: a novel p53-binding protein with some functional properties of MDM2
    A Shvarts, W T Steegenga, N Riteco, T van Laar, P Dekker, M Bazuine, R C van Ham, W van der Houven van Oordt, G Hateboer, A J van der Eb, and A G Jochemsen

    EMBO J. 1996 October 1; 15(19): 5349–5357


  • A 200 bp region of the pea ENOD12 promoter is sufficient for nodule-specific and Nod factor induced expression
    Vijn I, Christiansen H, Lauridsen P, Kardailsky I, et al.

    Plant molecular biology 28 (6), 1103-1110

  • A microtiter plate-based high-throughput DNA purification method
    K. Wang, L. Gan, C. Boysen, and L. Hood

    Anal. Biochem. 226, 85-90, 1995

  • A new Lectin-Type Glycoprotein Identified in the Peribacteroid Fluid of Pea Nodules
    IV Kardailsky, NJ Brewin

    Advances in Molecular Genetics of Plant-Microbe Interactions Current Plant Science and Biotechnology in Agriculture Volume 21, 1994, pp 139-142

  • Differentiation of the symbiosome compartment in pea nodule cells
    NJ Brewin, L Bolaños, P Dahiya, CD Gardner, LE Hernández, IV Kardailsky, EA Rathbun, DJ Sherrier

    Nitrogen Fixation: Fundamentals and Applications Current Plant Science and Biotechnology in Agriculture Volume 27, 1995, pp 455-460

  • Pairwise end sequencing: a unified approach to genomic mapping and sequencing
    J. C. Roach, C. Boysen, K. Wang, and L. Hood

    Genomics 26, 345-353, 1995

  • PZF, a cDNA isolated from Lotus japonicus and soybean root nodule libraries, encodes a new plant member of the RING-finger family of zinc-binding proteins
    Schauser L, Christensen L, Borg S, Poulsen C

    Plant Physiol. 1995 Apr;107(4):1457-8

  • The Rhizobium-legume interface in pea root nodules: studies of nodulins, glycoproteins and proteases
    IV Kardailsky

    Ph. D. thesis, University of East Anglia, Norwich. UK


  • Bacterial and plant glycoconjugates at the Rhizobium-legume interface
    Brewin NJ, Rae AL, Perotto S, Kannenberg EL, Rathbun EA, Lucas MM, Gunder A, Bolaños L, Kardailsky IV, Wilson KE, et al.

    Biochemical Society symposium 1994;60:61-73


  • Mechanisms of cell and tissue invasion by Rhizobium leguminosarum: the role of cell surface interactions
    Brewin NJ, Perotto S, Kannenberg EL, Rae AL, Rathbun EA, Lucas MM, Kardailsky I, Gunder A, Bolanos L, Donovan N

    Current Plant Science and Biotechnology in Agriculture 1993, 14:369-380;jsessionid=9o4dZDgS4k9N49Wlq92a.0

  • The pea late nodulin gene PsNOD6 is homologous to the early nodulin genes PsENOD3/14 and is expressed after the leghaemoglobin genes
    I Kardailsky, WC Yang, A Zalensky, A Kammen, T Bisseling

    Plant molecular biology 23 (5), 1029-1037


  • A comprehensive genetic linkage map of the human genome
    NIH/CEPH collaborative mapping group. H. Donis-Keller, R. Weaver, S. Ramachandra, C. Warlick, A. K. Burgess, J. L. Weber, M. Litt, D. A. Nickerson, C. A. Boysen, L. Hood, and S. K. Mishra: Chromosome 14

    Science, 67-86, 1992

  • Identification of clusters of biallelic polymorphic sequence-tagged sites (pSTSs) that generate highly informative and automatable markers for genetic linkage mapping
    D. A. Nickerson, C. Whitehurst, C. Boysen, P. Charmley, R. Kaiser, and L. Hood

    Genomics 12, 377-387, 1992


  • Genes of pea (Pisum sativum) forming the symbiotic association with nitrogen-fixing bacteria. II. The nucleotide sequences of the cDNA and of the part of genomic DNA of late nodulin gene Nod6 (PsNod6)
    IV Kardailsky, F Govers, T Bisseling, I Tikhonovich, A Zalensky

    Molekulyarnaya Biologiya 25 (1991) 6 DOI:46161