Center for Biological Sequence Analysis

  1. 2013
  2. Published

    31P gain of chromosomal region 15q26 cause increased expression of blm and fanci, and is associated with sensitivity to platinum chemotherapy in triple negative breast cancer. / Birkbak, Nicolai Juul; Li, Y.; Bowman-Collin, C.; Iglehart, J.D.; Silver, D.; Wang, Z.C.; Szallasi, Zoltan Imre; Richardson, A.

    In: Annals of Oncology, Vol. 24, No. suppl 3, 2013, p. iii22.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  3. Published
  4. Published
  5. Published
  6. Published

    Analyzing Plasmodium falciparum erythrocyte membrane protein 1 gene expression by a next generation sequencing based method. / Jespersen, Jakob S.; Petersen, Bent; Seguin-Orlando, Andaine; Willerslev, Eske; Gilbert, M. Thomas P.; Lusingu, John; Theander, Thor G.; Lavstsen, Thomas.

    In: The nature of parasitism: Joint Spring Symposium 2013, Danish Society for Parasitology and Danish Society for Tropical Medicine & International Health. 2013. p. 8.

    Publication: Research - peer-reviewConference abstract in proceedings – Annual report year: 2013

  7. Published

    A Unified Model of the GABA(A) Receptor Comprising Agonist and Benzodiazepine Binding Sites. / Kongsbak, Kristine Grønning; Bergmann, Rikke; Sørensen, Pernille Louise; Sander, Tommy; Balle, Thomas.

    In: P L o S One, Vol. 8, No. 1, 2013, p. e52323.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  8. Published

    Bioinformatics Identification of Antigenic Peptide: Predicting the Specificity of Major MHC Class I and II Pathway Players.. / Lund, Ole; Karosiene, Edita; Lundegaard, Claus; Larsen, Mette Voldby; Nielsen, Morten.

    In: Antigen Processing : Methods and Protocols. 2013. p. 247-260 (Methods in Molecular Biology, Vol. 960).

    Publication: Research - peer-reviewBook chapter – Annual report year: 2013

  9. Published
  10. Published

    CMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomics.. / Vesth, Tammi Camilla; Lagesen, Karin; Acar, Öncel; Ussery, David.

    In: P L o S One, Vol. 8, No. 4, 2013, p. e60120.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  11. Published

    Content and distribution of phytanic acid diastereomers in organic milk as affected by feed composition. / Che, Brita Ngum; Kristensen, Troels; Nebel, Caroline; Dalsgaard, Trine; Hellgren, Lars; Young, Jette Feveile; Larsen, Mette K.

    In: Journal of Agricultural and Food Chemistry, Vol. 61, No. 1, 2013, p. 225-230.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  12. Published

    Discovery of a novel selective PPARγ ligand with partial agonist binding properties by integrated in silico / in vitro work flow. / Kouskoumvekaki, Irene; Petersen, Rasmus K.; Fratev, Filip Filipov ; Taboureau, Olivier ; Nielsen, Thomas Eiland; Oprea, Tudor; Sonne, Si Brask; Flindt, Esben N.; Jonsdottir, Svava Osk; Kristiansen, Karsten.

    In: Journal of Chemical Information and Modeling, Vol. 53, No. 4, 2013, p. 923-937.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  13. Published

    From essential to persistent genes: a functional approach to constructing synthetic life. / Acevedo-Rocha, Carlos G.; Fang, Gang; Schmidt, Markus; Ussery, David; Danchin, Antoine.

    In: Trends in Genetics, Vol. 29, No. 5, 2013, p. 273-279.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  14. Published
  15. Published

    Genome-wide assessment of the association of rare and common copy number variations to testicular germ cell cancer.. / Edsgard, Stefan Daniel; Dalgaard, Marlene Danner; Weinhold, Nils; Wesolowska, Agata; Rajpert-De Meyts, Ewa; Ottesen, Anne Marie; Juul, Anders; Skakkebæk, Niels Erik; Jensen, Thomas Skøt; Gupta, Ramneek; Leffers, Henrik; Brunak, Søren.

    In: Frontiers in Endocrinology, Vol. 4, 2013.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  16. Published
  17. Published
  18. Published

    Identification of LasR Ligands through a Virtual Screening Approach. / Skovstrup, Søren; Le Quement, Sebastian Thordal; Hansen, Thomas; Jakobsen, Tim Holm; Harmsen, Morten; Tolker‐Nielsen, Tim; Nielsen, Thomas Eiland; Givskov, Michael Christian; Taboureau, Olivier .

    In: ChemMedChem, Vol. 8, No. 1, 2013, p. 157-163.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  19. Published

    Identification of peptides from foot‐and‐mouth disease virus structural proteins bound by class I swine leukocyte antigen (SLA) alleles, SLA‐1*0401 and SLA‐2*0401. / Pedersen, Lasse Eggers; Harndahl, M.; Nielsen, Morten; Patch, J. R.; Jungersen, Gregers; Buus, S.; Golde, W. T.

    In: Animal Genetics, Vol. 44, No. 3, 2013, p. 251-258.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  20. Published

    Identification of Y-Chromosomally Encoded Minor Histocompatibility Antigens Using a Reverse Immunology Approach. / Mortensen, Bo Kok; Brændstrup, Peter; Larsen, Malene Erup; Larsen, Mette Voldby; Lund, Ole; Rasmussen, Michael; Buus, Søren; Stryhn, Anette; Vindeløv, Lars.

    In: Biology of Blood and Marrow Transplantation, Vol. 19, No. 2, 2013, p. S335.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2013

  21. Published

    In Vivo SILAC-Based Proteomics Reveals Phosphoproteome Changes during Mouse Skin Carcinogenesis. / Zanivan, Sara; Meves, Alexander; Behrendt, Kristina; Schoof, Erwin; Neilson, Lisa J.; Cox, Jürgen; Tang, Hao R.; Kalna, Gabriela; van Ree, Janine H.; van Deursen, Jan M.; Trempus, Carol S.; Machesky, Laura M.; Linding, Rune; Wickström, Sara A.; Fässler, Reinhard; Mann, Matthias.

    In: Cell Reports, Vol. 3, No. 2, 2013, p. 552-566.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  22. Published

    Lipid hydrolysis products affect the composition of microbiota isolated from infant fecal samples after in vitro fermentation. / Bennike, Rikke Mette Guldhammer; Licht, Tine Rask; Hellgren, Lars.

    2013. Abstract from Cell Symposia, Lisbon, Portugal.

    Publication: Research - peer-reviewConference abstract for conference – Annual report year: 2013

  23. Published

    Lipid hydrolysis products affect the composition of microbiota isolated from infant fecal samples after in vitro fermentation. / Bennike, Rikke Mette Guldhammer; Licht, Tine Rask; Hellgren, Lars.

    2013. Abstract from 27th Nordic Lipid Symposium, Helsinki, Finland.

    Publication: ResearchConference abstract for conference – Annual report year: 2013

  24. Published

    Peptide-binding motifs associated with MHC molecules common in Chinese rhesus macaques are analogous to those of human HLA supertypes and include HLA-B27-like alleles. / Mothé, Bianca R.; Southwood, Scott; Sidney, John; English, A. Michelle; Wriston, Amanda; Hoof, Ilka; Shabanowitz, Jeffrey; Hunt, Donald F.; Sette, Alessandro.

    In: Immunogenetics, Vol. 65, No. 5, 2013, p. 371-386.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  25. Published

    Postnatal amniotic fluid intake reduces gut inflammatory responses and necrotizing enterocolitis in preterm neonates. / Siggers, Jayda; Østergaard, Mette V.; Siggers, Richard H.; Skovgaard, Kerstin; Mølbak, Lars; Thymann, Thomas; Schmidt, Mette; Møller, Hanne Kristine; Purup, Stig; Fink, Lisbeth Nielsen; Frøkiær, Hanne; Boye, Mette; Sangild, Per T.; Bering, Stine B.

    In: American Journal of Physiology: Gastrointestinal and Liver Physiology, Vol. 304, No. 10, 2013, p. G864-G875.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  26. Published

    Predictions of Phase Separation in Three-Component Lipid Membranes by the MARTINI Force Field. / Davis, Ryan S.; Sunil Kumar, P. B.; Sperotto, Maria Maddalena; Laradji, Mohamed.

    In: Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, Vol. 117, 2013, p. 4072-4080.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  27. Published

    Prognostic and Predictive Markers in Metastatic Renal Cell Carcinoma. / Khattak, Muhammad A.; Bakr, Farrah; Krzystanek, Marcin; Szallasi, Zoltan Imre; Gerlinger, Marco; Santos, Claudio; Swanton, Charles; Pickering, Lisa M.; Gore, Martin E.; Larkin, James M.G.

    In: Journal of Clinical Oncology, Vol. 31, No. 7, 2013, p. 20971-972.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  28. Published

    Reply to 'Mining electronic health records: an additional perspective'. / Jensen, Peter B.; Jensen, Lars J.; Brunak, Søren.

    In: Nature Reviews. Genetics, Vol. 14, No. 1, 2013, p. -.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  29. Published

    Structural analysis of B-cell epitopes in antibody:protein complexes. / Kringelum, Jens Vindahl; Nielsen, Morten; Padkjær, Søren Berg; Lund, Ole.

    In: Molecular Immunology, Vol. 53, No. 1-2, 2013, p. 24-34.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  30. Published

    Targeted Metabolic Engineering Guided by Computational Analysis of Single-Nucleotide Polymorphisms (SNPs).. / Udatha, D B R K Gupta; Rasmussen, Simon; Sicheritz-Pontén, Thomas; Panagiotou, Gianni.

    In: Systems Metabolic Engineering : Methods and Protocols. Springer Science+Business Media B.V., 2013. (Methods in Molecular Biology, Vol. 985).

    Publication: Research - peer-reviewBook chapter – Annual report year: 2013

  31. Published
  32. Published

    Transcriptome Responses to Combinations of Stresses in Arabidopsis. / Rasmussen, Simon; Barah, Pankaj; Suarez-Rodriguez, Maria Cristina; Bressendorff, Simon; Friis, Pia; Costantino, Paolo; Bones, Atle M.; Nielsen, Henrik Bjørn; Mundy, John.

    In: Plant Physiology, Vol. 161, No. 4, 2013, p. 1783-1794.

    Publication: Research - peer-reviewJournal article – Annual report year: 2013

  33. 2012
  34. Published

    Absorption difference between diacylglycerol oil and butter blend containing diacylglycerol oil. / Kristensen, Janni Brogaard; Jørgensen, Henry; Mu, Huiling.

    In: European Journal of Lipid Science and Technology, Vol. 114, No. 2, 2012, p. 146-152.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  35. Published

    A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens). / Hildebrand, Falk; Ebersbach, Tine; Nielsen, Henrik Bjørn; Li, Xiaoping; Sonne, Si Brask; dos Santos, Marcelo Bertalan Quintanilha; Dimitrov, Peter; Madsen, Lise; Qin, Junjie; Wang, Jun; Raes, Jeroen; Kristiansen, Karsten; Licht, Tine Rask.

    In: B M C Genomics, Vol. 13, No. 514, 2012.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  36. Published

    A genome-wide association study of men with symptoms of testicular dysgenesis syndrome and its network biology interpretation.. / Dalgaard, Marlene D; Weinhold, Nils; Edsgard, Stefan Daniel; Silver, Jeremy D; Pers, Tune Hannes; Nielsen, John E.; Jørgensen, Niels; Juul, Anders; Gerds, Thomas A.; Giwercman, Aleksander; Giwercman, Yvonne L.; Cohn-Cedermark, Gabriella; Virtanen, Helena E.; Toppari, Jorma; Daugaard, Gedske; Jensen, Thomas Skøt; Brunak, Søren; Rajpert-De Meyts, Ewa; Skakkebæk, Niels E; Leffers, Henrik; Gupta, Ramneek.

    In: Journal of Medical Genetics, Vol. 49, No. 1, 2012, p. 58-65.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  37. Published
  38. Published

    Androgen receptor signalling in peritubular myoid cells is essential for normal differentiation and function of adult Leydig cells. / Welsh, M.; Moffat, L.; Belling, Kirstine Christensen; de Franca, L. R.; Segatelli, T. M.; Saunders, P. T. K.; Sharpe, R. M.; Smith, L. B.

    In: International Journal of Andrology, Vol. 35, No. 1, 2012, p. 25-40.

    Publication: Research - peer-reviewJournal article – Annual report year: 2011

  39. Published

    Applied systems biology - vanillin production in Saccharomyces cerevisiae. / Strucko, Tomas; Eriksen, Carsten; Nielsen, J.; Mortensen, Uffe Hasbro.

    In: The F E B S Journal (Online), Vol. 279, No. Supplement s1, 2012, p. 525-525.

    Publication: Research - peer-reviewConference abstract in journal – Annual report year: 2012

  40. Published

    Association between chemical pattern in breast milk and congenital cryptorchidism: modelling of complex human exposures. / Krysiak-Baltyn, Konrad; Toppari, J.; Skakkebaek, N. E.; Jensen, Thomas Skøt; Virtanen, H. E.; Schramm, K.‐W.; Shen, Hao; Vartiainen, T.; Kiviranta, H.; Taboureau, Olivier ; Audouze, Karine Marie Laure; Brunak, S.; Main, K. M.

    In: International Journal of Andrology, Vol. 35, No. 3, 2012, p. 294-302.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  41. Published

    A Steered Molecular Dynamics Study of Binding and Translocation Processes in the GABA Transporter. / Skovstrup, Soren; David, Laurent; Taboureau, Olivier; Jorgensen, Flemming Steen.

    In: P L o S One, Vol. 7, No. 6, 2012, p. -.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  42. Published

    Bacterial adaptive response to changing herbicide discharge rates in the streambed sediments impacted by a landfill. / Pazarbasi, Meric Batioglu; Bælum, Jacob; Pilloni, Giovanni; Larentis, Micheal; Jacobsen, Carsten S.; Lueders, Tillmann; Hansen, Lars H.; Aamand, Jens .

    2012. Poster session presented at 14th International Symposium on Microbial Ecology, Copenhagen, Denmark.

    Publication: Research - peer-reviewPoster – Annual report year: 2012

  43. Published

    Bayesian prediction of bacterial growth temperature range based on genome sequences. / Jensen, Dan Børge; Vesth, Tammi Camilla; Hallin, Peter Fischer; Pedersen, Anders Gorm; Ussery, David.

    In: Eleventh International Conference on Bioinformatics (InCoB2012): Computational Biology. Vol. 13 2012. (B M C Genomics).

    Publication: Research - peer-reviewArticle in proceedings – Annual report year: 2012

  44. Published

    BDDCS Class Prediction for New Molecular Entities. / Broccatelli, Fabio; Cruciani, Gabriele; Benet, Leslie Z.; Oprea, Tudor.

    In: Molecular Pharmaceutics, Vol. 9, No. 3, 2012, p. 570-580.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  45. Published

    Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers. / Schneider, Maria V.; Walter, Peter; Blatter, Marie-Claude; Watson, James; Brazas, Michelle D.; Rother, Kristian; Budd, Aidan; Via, Allegra; van Gelder, Celia W. G.; Jacob, Joachim; Fernandes, Pedro; Nyrönen, Tommi H.; De Las Rivas, Javier; Holberg Blicher, Thomas; Jimenez, Rafael C.; Loveland, Jane; McDowall, Jennifer; Jones, Phil; Vaughan, Brendan W.; Lopez, Rodrigo; Attwood, Teresa K.; Brooksbank, Catherine.

    In: Briefings in Bioinformatics, Vol. 13, No. 3, 2012, p. 383-389.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  46. Published

    Campylobacter fetus subspecies: Comparative genomics and prediction of potential virulence targets. / Ali, Amjad; Soares, Siomar C.; Santos, Anderson R.; Guimarães, Luis C.; Barbosa, Eudes; Almeida, Sintia S.; Abreu, Vinícius A.C.; Carneiro, Adriana R.; Ramos, Rommel T.J.; Bakhtiar, Syeda Marriam; Hassan, Syed S.; Ussery, David W.; On, Stephen; Silva, Artur; Schneider, Maria P.; Lage, Andrey P.; Miyoshi, Anderson; Azevedo, Vasco.

    In: Gene, Vol. 508, No. 2, 2012, p. 145-156.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  47. Published

    Cells, shared memory and breaking the PTM code.. / Creixell, Pau; Linding, Rune.

    In: Molecular Systems Biology, Vol. 8, 2012.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  48. Published

    Ceramide profile in hypohidrotic ectodermal dysplasia. / Jungersted, J. M.; Høgh, Julie Kaae; Hellgren, Lars; Agner, T.; Jemec, G. B. E.

    In: Clinical and Experimental Dermatology, Vol. 37, No. 2, 2012, p. 153-155.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  49. Published

    CERT depletion predicts chemotherapy benefit and mediates cytotoxic and polyploid‐specific cancer cell death through autophagy induction. / Lee, Alvin J. X.; Roylance, Rebecca; Sander, Jil; Gorman, Patricia; Endesfelder, David; Kschischo, Maik; Jones, Neil P.; East, Philip; Nicke, Barbara; Spassieva, Stefka; Obeid, Lina M.; Birkbak, Nicolai Juul; Szallasi, Zoltan; McKnight, Nicole C.; Rowan, Andrew J.; Speirs, Valerie; Hanby, Andrew M.; Downward, Julian; Tooze, Sharon A.; Swanton, Charles.

    In: Journal of Pathology, Vol. 226, No. 3, 2012, p. 482-494.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  50. Published

    Characterization of HIV-Specific CD4+T Cell Responses against Peptides Selected with Broad Population and Pathogen Coverage. / Buggert, Marcus; Norstrom, Melissa M.; Czarnecki, Chris; Tupin, Emmanuel; Luo, Ma; Gyllensten, Katarina; Sonnerborg, Anders; Lundegaard, Claus; Lund, Ole; Nielsen, Morten; Karlsson, Annika C.

    In: P L o S One, Vol. 7, No. 7, 2012.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  51. Published

    Characterizing the binding motifs of 11 common human HLA‐DP and HLA‐DQ molecules using NNAlign. / Andreatta, Massimo; Nielsen, Morten.

    In: Immunology, Vol. 136, No. 3, 2012, p. 306-311.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

  52. 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, Jesper Roland; Fransson, Anette; Fjord-Larsen, Lone; Thompson, Lachlan H.; Houchins, Jeffrey P.; Andrade, Nuno; Torp, Malene; Kalkkinen, Nisse; Andersson, Elisabet; Lindvall, Olle; Ulfendahl, Mats; Brunak, Søren; Johansen, Teit E.; Wahlberg, Lars U.

    In: Experimental Neurology, Vol. 233, No. 1, 2012, p. 172-181.

    Publication: Research - peer-reviewJournal article – Annual report year: 2012

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