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2014 Journal Article Insight into hyaluronic acid molecular weight controlMarcellin, Esteban, Steen, Jennifer A. and Nielsen, Lars K. (2014). Insight into hyaluronic acid molecular weight control. Applied Microbiology and Biotechnology, 98 (16), 6947-6956. doi: 10.1007/s00253-014-5853-x |
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2014 Journal Article A depth-first search algorithm to compute elementary flux modes by linear programmingQuek, Lake-Ee and Nielsen, Lars K (2014). A depth-first search algorithm to compute elementary flux modes by linear programming. BMC Systems Biology, 8 (1) 94. doi: 10.1186/s12918-014-0094-2 |
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2014 Journal Article Network thermodynamic curation of human and yeast genome-scale metabolic modelsMartinez, Veronica S., Quek, Lake-Ee and Nielsen, Lars K. (2014). Network thermodynamic curation of human and yeast genome-scale metabolic models. Biophysical Journal, 107 (2), 493-503. doi: 10.1016/j.bpj.2014.05.029 |
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2014 Journal Article Temporal dynamics of the Saccharopolyspora erythraea phosphoproteomeLicona-Cassani, Cuauhtemoc, Lim, SooA, Marcellin, Esteban and Nielsen, Lars K. (2014). Temporal dynamics of the Saccharopolyspora erythraea phosphoproteome. Molecular and Cellular Proteomics, 13 (5), 1219-1230. doi: 10.1074/mcp.M113.033951 |
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2014 Journal Article RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE)Ohmiya, Hiroko, Vitezic, Morana, Frith, Martin C., Itoh, Masayoshi, Carninci, Piero, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Lassmann, Timo, FANTOM Consortium, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Mason, Elizabeth, Wolvetang, Ernst, Hitchens, Kelly, Le Cao, Kim-Anh, Nielsen, Lars, Fearnley, Liam, Kenna, Tony and Blumenthal, Antje (2014). RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE). BMC Genomics, 15 (1) 269. doi: 10.1186/1471-2164-15-269 |
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2014 Journal Article Redefinition of the human mast cell transcriptome by deep-CAGE sequencingMotakis, Efthymios, Guhl, Sven, Ishizu, Yuri, Itoh, Masayoshi, Kawaji, Hideya, de Hoon, Michiel, Lassman, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Zuberbier, Torsten, Forrest, Alistair R. R., Babina, Magda, for The FANTOM Consortium, Wells, Christine, Wolvetang, Ernst, Beckhouse, Anthony, Fearnley, Liam, Hitchens, Kelly, Kenna, Tony, Le Cao, Kim-Anh, Mason, Elizabeth, Nielsen, Lars, Vijayan, Dipti, Blumenthal, Antje, Ovchinnikov, Dmitry and Briggs, James (2014). Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. Blood, 123 (17), 58-67. doi: 10.1182/blood-2013-02-483792 |
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2014 Journal Article Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylationRönnerblad, Michelle, Andersson, Robin, Olofsson, Tor, Douagi, Iyadh, Karimi, Mohsen, Lehmann, Sören, Hoof, Ilka, de Hoon, Michiel, Itoh, Masayoshi, Nagao-Sato, Sayaka, Kawaji, Hideya, Lassmann, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Sandelin, Albin, Ekwall, Karl, Amer, Erik, Lennartsson, Andreas, for the FANTOM consortium, Wells, Christine, Wolvetang, Ernst, Blumenthal, Antje, Kenna, Tony, Hitchens, Kelly, Ovchinnikov, Dmitry, Fearnley, Liam, Le Cao, Kim-Anh, Mason, Elizabeth ... Vijayan, Dipti (2014). Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation. Blood, 123 (17), e79-e89. doi: 10.1182/blood-2013-02-482893 |
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2014 Journal Article Transcription and enhancer profiling in human monocyte subsetsSchmidl, Christian, Renner, Kathrin, Peter, Katrin, Eder, Ruediger, Lassmann, Timo, Balwierz, Piotr J., Itoh, Masayohshi, Nagao-Sato, Sayaka, Kawaji, Hideya, Carninci, Piero, Suzuki, Harukazu, Hayashizaki, Yoshihide, Andreesen, Reinhard, Hume, David A., Hoffmann, Petra, Forrest, Alistair R. R., Kreutz, Marina P., Edinger, Matthias, Rehli, Michael, for the FANTOM consortium, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Mason, Elizabeth, Wolvetang, Ernst, Hitchens, Kelly, Le Cao, Kim-Anh, Nielsen, Lars, Fearnley, Liam and Kenna, Tony (2014). Transcription and enhancer profiling in human monocyte subsets. Blood, 123 (17), e90-e99. doi: 10.1182/blood-2013-02-484188 |
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2014 Journal Article Concise review: next-generation cell therapies to prevent infections in neutropenic patientsBrunck, Marion E. G. and Nielsen, Lars K. (2014). Concise review: next-generation cell therapies to prevent infections in neutropenic patients. Stem Cells Translational Medicine, 3 (4), 541-548. doi: 10.5966/sctm.2013-0145 |
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2014 Journal Article Interactive visualization and analysis of large-scale sequencing datasets using ZENBUSeverin, Jessica, Lizio, Marina, Harshbarger, Jayson, Kawaji, Hideya, Daub, Carsten O., Hayashizaki, Yoshihide, Bertin, Nicolas, Forrest, Alistair R. R., FANTOM Consortium, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Mason, Elizabeth, Wolvetang, Ernst, Hitchens, Kelly, Le Cao, Kim-Anh, Nielsen, Lars, Fearnley, Liam and Kenna, Tony (2014). Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. Nature Biotechnology, 32 (3), 217-219. doi: 10.1038/nbt.2840 |
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2014 Journal Article The trehalose phosphotransferase system (PTS) in E. coli W can transport low levels of sucrose that are sufficient to facilitate induction of the csc sucrose catabolism operonSteen, Jennifer A., Bohlke, Nina, Vickers, Claudia E. and Nielsen, Lars K. (2014). The trehalose phosphotransferase system (PTS) in E. coli W can transport low levels of sucrose that are sufficient to facilitate induction of the csc sucrose catabolism operon. PLoS One, 9 (2) e88688, e88688.1-e88688.10. doi: 10.1371/journal.pone.0088688 |
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2014 Journal Article A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulatorsHurst, Laurence D., Sachenkova, Oxana, Daub, Carsten, Forrest, Alistair R. R., the FANTOM consortium, Huminiecki, Lukasz, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Wolvetang, Ernst, Hitchens, Kelly, Kenna, Tony, Blumenthal, Antje, Briggs, James, Ovchinnikov, Dmitry, Fearnley, Liam, Le Cao, Kim-Anh, Mason, Elizabeth and Nielsen, Lars (2014). A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators. Genome Biology, 15 (7) 413. doi: 10.1186/s13059-014-0413-3 |
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2014 Journal Article Targeted sequencing for gene discovery and quantification using RNA CaptureSeqMercer, Tim R., Clark, Michael B., Crawford, Joanna, Brunck, Marion E., Gerhardt, Daniel J., Taft, Ryan J., Nielsen, Lars K., Dinger, Marcel E. and Mattick, John S. (2014). Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. Nature Protocols, 9 (5), 989-1009. doi: 10.1038/nprot.2014.058 |
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2014 Journal Article Allantoin catabolism influences the production of antibiotics in Streptomyces coelicolorNavone, Laura, Casati, Paula, Licona-Cassani, Cuauhtémoc, Marcellin, Esteban, Nielsen, Lars K., Rodriguez, Eduardo and Gramajo, Hugo (2014). Allantoin catabolism influences the production of antibiotics in Streptomyces coelicolor. Applied Microbiology and Biotechnology., 98 (1), 351-360. doi: 10.1007/s00253-013-5372-1 |
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2014 Journal Article The effect of cell line, phylogenetics and medium on baculovirus budded virus yield and qualityMatindoost, Leila, Hu, Hao, Chan, Leslie C. L., Nielsen, Lars K. and Reid, Steven (2014). The effect of cell line, phylogenetics and medium on baculovirus budded virus yield and quality. Archives of Virology, 159 (1), 91-102. doi: 10.1007/s00705-013-1789-1 |
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2014 Journal Article A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiationTomaru, Yasuhiro, Hasegawa, Ryota, Suzuki, Takahiro, Sato, Taiji, Kubosaki, Atsutaka, Suzuki, Masanori, Kawaji, Hideya, Forrest, Alistair R. R., Hayashizaki, Yoshihide, FANTOM Consortium, Shin, Jay W., Suzuki, Harukazu, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Wolvetang, Ernst, Hitchens, Kelly, Fearnley, Liam, Kenna, Tony, Blumenthal, Antje, Briggs, James, Ovchinnikov, Dmitry, Le Cao, Kim-Anh, Mason, Elizabeth and Nielsen, Lars (2014). A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation. Nucleic Acids Research, 42 (14), 8905-8913. doi: 10.1093/nar/gku567 |
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2014 Journal Article Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like moleculesGrison, Alice, Zucchelli, Silvia, Urzi, Alice, Zamparo, Ilaria, Lazarevic, Dejan, Pascarella, Giovanni, Roncaglia, Paola, Giorgetti, Alejandro, Garcia-Esparcia, Paula, Vlachouli, Christina, Simone, Roberto, Persichetti, Francesca, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Carloni, Paolo, Ferrer, Isidro, Lodovichi, Claudia, Plessy, Charles, the FANTOM Consortium, Carninci, Piero, Gustincich, Stefano, Beckhouse, Anthony, Briggs, James, Hitchens, Kelly, Kenna, Tony, Ovchinnikov, Dmitry, Vijayan, Dipti, Wells, Christine, Wolvetang, Ernst ... Nielsen, Lars (2014). Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules. BMC Genomics, 15 (1) 729. doi: 10.1186/1471-2164-15-729 |
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2013 Journal Article Chemical inhibition of acetyl coenzyme A carboxylase as a strategy to increase polyhydroxybutyrate yields in transgenic sugarcanePetrasovits, Lars A., McQualter, Richard B., Gebbie, Leigh K., Blackman, Deborah M., Nielsen, Lars K. and Brumbley, Stevens M. (2013). Chemical inhibition of acetyl coenzyme A carboxylase as a strategy to increase polyhydroxybutyrate yields in transgenic sugarcane. Plant Biotechnology Journal, 11 (9), 1146-1151. doi: 10.1111/pbi.12109 |
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2013 Journal Article Genome scale transcriptomics of baculovirus-insect interactionsNguyen,Quan, Nielsen, Lars K. and Reid, Steven (2013). Genome scale transcriptomics of baculovirus-insect interactions. Viruses, 5 (11), 2721-2747. doi: 10.3390/v5112721 |
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2013 Journal Article Dual gene expression cassette vectors with antibiotic selection markers for engineering in Saccharomyces cerevisiaeVickers C.E., Bydder S.F., Zhou Y. and Nielsen L.K. (2013). Dual gene expression cassette vectors with antibiotic selection markers for engineering in Saccharomyces cerevisiae. Microbial Cell Factories, 12 (96) 96, 96.1-96.11. doi: 10.1186/1475-2859-12-96 |
