Center for Biological Sequence Analysis
- 2013
- 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-review › Journal article – Annual report year: 2013
- Published
45p deciphering patterns of chromosomal aberrations in breast cancer patients: how defects in specific dna repair genes affect the accumulation of gross dna aberrations in the cancer genome. / Marquard, Andrea Marion; Birkbak, Nicolai Juul; Eklund, Aron Charles; Varga, A.; Szüts, D.; Szallasi, Zoltan Imre.
In: Annals of Oncology, Vol. 24, No. suppl 3, 2013, p. iii26.Publication: Research - peer-review › Journal article – Annual report year: 2013
- Published
Accurate prediction of secondary metabolite gene clusters in filamentous fungi.. / Andersen, Mikael Rørdam; Nielsen, Jakob Blæsbjerg; Klitgaard, Andreas; Petersen, Lene Maj; Zachariasen, Mia; Hansen, Tilde J; Holberg Blicher, Lene; Gotfredsen, Charlotte Held; Larsen, Thomas Ostenfeld; Nielsen, Kristian Fog; Mortensen, Uffe Hasbro.
In: National Academy of Sciences. Proceedings, Vol. 110, No. 1, 2013, p. E99-E107.Publication: Research - peer-review › Journal article – Annual report year: 2013
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A conceptual model linking functional gene expression and reductive dechlorination rates of chlorinated ethenes in clay rich groundwater sediment. / Bælum, Jacob; Chambon, Julie Claire Claudia; Scheutz, Charlotte; Binning, Philip John; Laier, Troels; Bjerg, Poul Løgstrup; Jacobsen, Carsten.
In: Water Research, Vol. 47, No. 7, 2013, p. 2467-2478.Publication: Research - peer-review › Journal article – Annual report year: 2013
- 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-review › Conference abstract in proceedings – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Book chapter – Annual report year: 2013
- Published
ChemProt-2.0: visual navigation in a disease chemical biology database. / Kjærulff, Sonny Kim; Wich, Louis; Kringelum, Jens Vindahl; Jacobsen, Ulrik Plesner; Kouskoumvekaki, Irene; Audouze, Karine Marie Laure; Lund, Ole; Brunak, Søren; Oprea, Tudor; Taboureau, Olivier .
In: Nucleic Acids Research, Vol. 41, No. D1, 2013, p. D464-D469.Publication: Research - peer-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
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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-review › Journal article – Annual report year: 2013
- Published
Genome Sequencing Identifies Two Nearly Unchanged Strains of Persistent Listeria monocytogenes Isolated at Two Different Fish Processing Plants Sampled 6 Years Apart. / Holch, Anne; Webb, Kristen; Lukjancenko, Oksana; Ussery, David; Rosenthal, Benjamin M.; Gram, Lone.
In: Applied and Environmental Microbiology, Vol. 79, No. 9, 2013, p. 2944-2951.Publication: Research - peer-review › Journal article – Annual report year: 2013
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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-review › Journal article – Annual report year: 2013
- Published
Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. / Zankari, Ea; Hasman, Henrik; Kaas, Rolf Sommer; Seyfarth, Anne Mette; Agersø, Yvonne; Lund, Ole; Larsen, Mette Voldby; Aarestrup, Frank Møller.
In: Journal of Antimicrobial Chemotherapy, Vol. 68, No. 4, 2013, p. 771-777.Publication: Research - peer-review › Journal article – Annual report year: 2012
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HExpoChem: a systems biology resource to explore human exposure to chemicals. / Taboureau, Olivier ; Jacobsen, Ulrik Plesner; Kalhauge, Christian Gram; Edsgard, Stefan Daniel; Rigina, Olga; Gupta, Ramneek; Audouze, Karine Marie Laure.
In: Bioinformatics, Vol. 29, No. 9, 2013, p. 201231-1232.Publication: Research - peer-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
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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-review › Journal article – Annual report year: 2013
- 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-review › Conference abstract in journal – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
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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: Research › Conference abstract for conference – Annual report year: 2013
- 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-review › Conference abstract for conference – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013