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
- Published
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
- 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-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
- 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-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
- Published
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
- 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-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
- 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
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
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
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2013
- 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-review › Journal article – Annual report year: 2012
- 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-review › Book chapter – Annual report year: 2013
- Published
The chemical interactome space between the human host and the genetically defined gut metabotypes. / Jacobsen, Ulrik Plesner; Nielsen, Henrik Bjørn; Hildebrand, Falk; Raes, Jeroen; Sicheritz-Pontén, Thomas; Kouskoumvekaki, Irene; Panagiotou, Gianni.
In: I S M E Journal, Vol. 7, 2013, p. 730-742.Publication: Research - peer-review › Journal article – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2013
- 2012
- 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-review › Journal article – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2012
- Published
Analyzing the genomic variation of microbial cell factories in the era of “New Biotechnology”. / Herrgard, Markus; Panagiotou, Gianni.
In: Computational and Structural Biotechnology Journal, Vol. 3, No. 4, 2012.Publication: Research - peer-review › Journal article – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2011
- 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-review › Conference abstract in journal – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2012
- 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-review › Poster – Annual report year: 2012
- 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-review › Article in proceedings – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2012
- Published
Cells, shared memory and breaking the PTM code.. / Creixell, Pau; Linding, Rune.
In: Molecular Systems Biology, Vol. 8, 2012.Publication: Research - peer-review › Journal article – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2012
- 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-review › Journal article – Annual report year: 2012