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1. Full Text Updating benchtop sequencing performance comparison
by Jünemann, Sebastian and Sedlazeck, Fritz Joachim and Prior, Karola and Albersmeier, Andreas and John, Uwe and Kalinowski, Jörn and Mellmann, Alexander and Goesmann, Alexander and Von Haeseler, Arndt and Stoye, Jens and Harmsen, Dag
Nature biotechnology, ISSN 1087-0156, 04/2013, Volume 31, Issue 4, pp. 294 - 296
Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Sequence Analysis, DNA - instrumentation | Sequence Analysis, DNA - methods | Humans | DNA sequencers | Research | Nucleotide sequencing | DNA sequencing | Testing | Index Medicus
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2. Full Text Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment
by Schulte-Schrepping, Jonas and Reusch, Nico and Paclik, Daniela and Baßler, Kevin and Schlickeiser, Stephan and Krammer, Tobias and Brumhard, Sophia and Bonaguro, Lorenzo and Wendisch, Daniel and Grasshoff, Martin and Kapellos, Theodore S and Beckstette, Michael and Pecht, Tal and Saglam, Adem and Dietrich, Oliver and Mei, Henrik E and Schulz, Axel R and Conrad, Claudia and Kunkel, Désirée and Vafadarnejad, Ehsan and Xu, Cheng-Jian and Herbert, Miriam and Drews, Anna and Thibeault, Charlotte and Pfeiffer, Moritz and Hippenstiel, Stefan and Hocke, Andreas and Müller-Redetzky, Holger and Heim, Katrin-Moira and Bosquillon de Jarcy, Laure and Stegemann, Miriam and Glösenkamp, Christoph R and Volk, Hans-Dieter and Wyler, Emanuel and Georg, Philipp and Schneider, Maria and Dang-Heine, Chantip and Neuwinger, Nick and Kappert, Kai and Corman, Victor and Raabe, Jan and Kaiser, Kim Melanie and Rieke, Gereon and Meisel, Christian and Ulas, Thomas and Becker, Matthias and Drosten, Christian and Suttorp, Norbert and Kurth, Florian and Li, Yang and Nattermann, Jacob and Saliba, Antoine-Emmanuel and Sander, Leif Erik and Angelov, Angel and Bals, Robert and Bartholomäus, Alexander and Becker, Anke and Bonifacio, Ezio and Clavel, Thomas and Colome-Tatche, Maria and Diefenbach, Andreas and Dilthey, Alexander and Fischer, Nicole and Förstner, Konrad and Hain, Torsten and Hummel, Michael and Janssen, Stefan and Kallies, René and Kehr, Birte and Keller, Andreas and Kim-Hellmuth, Sarah and Klein, Christoph and Korbel, Jan O and Landthaler, Markus and Li, Yang and Ludwig, Kerstin and Marz, Manja and McHardy, Alice and Mertes, Christian and Nöthen, Markus and Nürnberg, Peter and Ohler, Uwe and Ossowski, Stephan and Overmann, Jörg and Peter, Silke and Pfeffer, Klaus and Poetsch, Anna R and Rajewsky, Nikolaus and Ralser, Markus and Saliba, Antoine-Emmanuel and Schulte, Eva-Christina and Schultze, Joachim L and Sczyrba, Alexander and Stoye, Jens and Theis, Fabian and Vogel, Jörg and von Kleist, Max and Walker, Andreas and Walter, Jörn and Wieczorek, Dagmar and Deutsche COVID-19 OMICS Initiative (DeCOI) and Deutsch COVID-19 OMICS Initiative
Cell (Cambridge), ISSN 0092-8674, 09/2020, Volume 182, Issue 6, pp. 1419 - 1440.e23
COVID-19 | monocytes | SARS-CoV-2 | scRNA-seq | emergency myelopoiesis | immune profiling | dysfunctional neutrophils | mass cytometry | neutrophils | Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Myeloid Cells - cytology | Proteome - genetics | Pandemics | Humans | Middle Aged | Male | CD11 Antigens - metabolism | Pneumonia, Viral - blood | CD11 Antigens - genetics | HLA-DR Antigens - genetics | Myeloid Cells - immunology | Coronavirus Infections - blood | Adult | Female | Myelopoiesis | Single-Cell Analysis | HLA-DR Antigens - metabolism | Pneumonia, Viral - pathology | Cells, Cultured | Coronavirus Infections - immunology | Pneumonia, Viral - immunology | Coronavirus Infections - pathology | Proteomics | Aged | Proteome - metabolism | Index Medicus
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3. Full Text Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome
by Kuenne, Carsten and Billion, André and Mraheil, Mobarak Abu and Strittmatter, Axel and Daniel, Rolf and Goesmann, Alexander and Barbuddhe, Sukhadeo and Hain, Torsten and Chakraborty, Trinad
BMC genomics, ISSN 1471-2164, 01/2013, Volume 14, Issue 1, pp. 47 - 47
Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Inverted Repeat Sequences - genetics | Rabbits | Genomic Islands - genetics | Species Specificity | Genomics | Humans | Listeria monocytogenes - virology | Phylogeny | Genome, Bacterial - genetics | Interspersed Repetitive Sequences - genetics | Listeria monocytogenes - pathogenicity | Animals | Adaptation, Physiological - genetics | Genetic Markers - genetics | DNA Transposable Elements - genetics | Conserved Sequence | Listeria monocytogenes - genetics | RNA, Small Untranslated - genetics | Models, Genetic | Internet | Listeria monocytogenes - physiology | Evolution, Molecular | Prophages - physiology | Proteins | Oxidative stress | Microbiology | Listeria | Mortality | Bacteria | Regulation | Genomes | Gene expression | Experiments | Index Medicus | Adaptations | Pathogens | Integration | RNA | Phages | Virulence | Listeriosis | Data processing | Evolutionary genetics | Single-nucleotide polymorphism | Host-pathogen interactions | Cores | Pathogenicity | Serotypes | Evolution | genomics | Models | Mutation | Prophages | transposon Tn916 | Islands | Niches | Food
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4. Full Text Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19
by Tran, Florian and Best, Lena and Blase, Johanna I and Bordoni, Dora and Josephs-Spaulding, Jonathan and Köhler, Philipp and Künstner, Axel and Rosati, Elisa and Aschenbrenner, Anna C and Bacher, Petra and Bruse, Niklas and Franzenburg, Sören and Frey, Norbert and Fuß, Janina and Glück, Andreas and Hamm, Jacob and Imm, Simon and Kaiser, Sina and Kan, Ying H and Lange, Christoph and Laue, Georg and Marinos, Georgios and Pickkers, Peter and Rabe, Klaus F and Renz, Alina and Röcken, Christoph and Rupp, Jan and Schaffarzyk, Annika and Scheffold, Alexander and Schulte-Schrepping, Jonas and Skowasch, Dirk and Ulas, Thomas and Wandinger, Klaus-Peter and Wittig, Michael and Zimmermann, Johannes and Busch, Hauke and Hoyer, Bimba F and Kaleta, Christoph and Heyckendorf, Jan and Rybniker, Jan and Schultze, Joachim L and Rosenstiel, Philip and Desai, Tushar and Eickelberg, Oliver and Haniffa, Muzlifa and Horvath, Peter and Kropski, Jonathan A and Lafyatis, Robert and Meyer, Kerstin and Nikolic, Marko and Ordovas Montanes, Jose and Pe’er, Dana and Tata, Purushothama Rao and Rawlins, Emma and Regev, Aviv and Reyfman, Paul and Samakovlis, Christos and Schultze, Joachim and Shalek, Alex and Shepherd, Douglas and Spence, Jason and Theis, Fabian and van den Berge, Maarten and von Papen, Michael and Whitsett, Jeffrey and Angelov, Angel and Bals, Robert and Bonifacio, Ezio and Colme-Tatche, Maria and Diefenbach, Andreas and Fischer, Nicole and Gagneur, Julien and Goesmann, Alexander and Kallies, René and Kehr, Birte and Keller, Andreas and Kim-Hellmuth, Sarah and Korbel, Jan O and Kurth, Ingo and Landthaler, Markus and Li, Yang and Ludwig, Kerstin and Makarewicz, Oliwia and Nöthen, Markus and Nürnberg, Peter and Ohler, Uwe and Overmann, Jörg and Peter, Silke and Pfeffer, Klaus and Poetsch, Anna R and Rajewsky, Niklaus and Ralser, Markus and Saliba, Antoine-Emmanuel and Schulte, Eva-Christina and Schultze, Joachim L and Sczyrba, Alexander and Stegle, Oliver and Stoye, Jens and von Kleist, Max and Walker, Andreas and HCA Lung Biological Network and the Deutsche COVID-19 Omics Initiative (DeCOI) and Deutsche COVID-19 Omics Initiative (DeCOI)
Immunity (Cambridge, Mass.), ISSN 1074-7613, 12/2020, Volume 53, Issue 6, pp. 1296 - 1314.e9
COVID-19 | scRNA-seq | acute respiratory distress | RNA-seq | immune response | infectious disease | methylation | disease trajectory | virus | blood | COVID-19 - immunology | Severity of Illness Index | Humans | Middle Aged | Cells, Cultured | Male | Gene Expression Profiling | Megakaryocytes - physiology | SARS-CoV-2 - physiology | Disease Progression | Plasma Cells - physiology | Sequence Analysis, RNA | COVID-19 - metabolism | Proteomics | Aged, 80 and over | Biomarkers | Adult | Erythroid Cells - pathology | Female | Aged | Single-Cell Analysis | Blood Circulation | Cohort Studies | Erythropoiesis | Flow cytometry | Transcription factors | Genomics | Viral diseases | Datasets | Peripheral blood | DNA methylation | Tumor necrosis factor-TNF | Temporal resolution | Megakaryocytes | Deoxyribonucleic acid--DNA | Immune system | Immune response | Cytokines | Neutrophils | Principal components analysis | Hospitalization | Coronaviruses | Erythroid cells | Gene expression | Patients | Severe acute respiratory syndrome coronavirus 2 | Hypoxia | Interferon | Index Medicus
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5. Full Text Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT
by Golyshina, Olga V and Tran, Hai and Reva, Oleg N and Lemak, Sofia and Yakunin, Alexander F and Goesmann, Alexander and Nechitaylo, Taras Y and Lacono, Violetta and Smedile, Francesco and Slesarev, Alexei and Rojo, David and Barbas, Coral and Ferrer, Manuel and Yakimov, Michail M and Golyshin, Peter N
Scientific reports, ISSN 2045-2322, 12/2017, Volume 7, Issue 1, pp. 1 - 12
Glycolysis | Pyruvic acid | Genomes | Mutation | Ferredoxin | Sugar | Fructose | a-Ketoglutaric acid | Gluconeogenesis
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6. Full Text Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia
by Blifernez-Klassen, Olga and Klassen, Viktor and Wibberg, Daniel and Cebeci, Enis and Henke, Christian and Rückert, Christian and Chaudhari, Swapnil and Rupp, Oliver and Blom, Jochen and Winkler, Anika and Al-Dilaimi, Arwa and Goesmann, Alexander and Sczyrba, Alexander and Kalinowski, Jörn and Bräutigam, Andrea and Kruse, Olaf
Scientific reports, 01/2021, Volume 11, Issue 1, pp. 1726 - 1726
Cell culture | Ecosystems | Algae | Cytology | Biotin | Food webs | Phylogeny | Auxotrophs | Consortia | Rhizosphere | Biosphere | Bacteria | Phytoplankton | Index Medicus
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7. Full Text Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism
by Yu, Jia and Blom, Jochen and Sczyrba, Alexander and Goesmann, Alexander
Journal of biotechnology, ISSN 0168-1656, 09/2017, Volume 257, pp. 58 - 60
Cloud computing | Parallel computing | Sequence alignment | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Computational Biology | Molecular Sequence Data | Sequence Alignment - instrumentation | Whole Genome Sequencing | Sequence Alignment - methods | Sequence Analysis, DNA - instrumentation | Cloud Computing | Comparative Genomic Hybridization | Software | High-Throughput Nucleotide Sequencing - instrumentation | Internet | Genomics - methods | High-Throughput Nucleotide Sequencing - methods | Metagenome | Sequence Analysis, DNA - methods | Nucleotide sequencing | Analysis | Genomics | DNA sequencing | Index Medicus
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8. Full Text EDGAR 2.0: an enhanced software platform for comparative gene content analyses
by Blom, Jochen and Kreis, Julian and Spänig, Sebastian and Juhre, Tobias and Bertelli, Claire and Ernst, Corinna and Goesmann, Alexander
Nucleic acids research, ISSN 0305-1048, 07/2016, Volume 44, Issue 1, pp. W22 - W28
Life Sciences & Biomedicine | Biochemistry & Molecular Biology | Science & Technology | Computational Biology - methods | Datasets as Topic | Species Specificity | Synteny | Conserved Sequence | Databases, Genetic | Computational Biology - statistics & numerical data | Microbial Consortia - genetics | Software | Internet | Phylogeny | Index Medicus | Web Server issue
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9. Full Text Visualization of omics data for systems biology
by Kitano, Hiroaki and Gavin, Anne-Claude and Gehlenborg, Nils and O'Donoghue, Seán I and Tenenbaum, Dan and Kohlbacher, Oliver and Baliga, Nitin S and Hibbs, Matthew A and Neuweger, Heiko and Schneider, Reinhard and Goesmann, Alexander
Nature methods, ISSN 1548-7091, 03/2010, Volume 7, Issue 3s, pp. S56 - S68
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biochemical Research Methods | Science & Technology | Metabolomics | Image Processing, Computer-Assisted | Genomics | Mass Spectrometry | Proteomics | Nuclear Magnetic Resonance, Biomolecular | Protein Binding | Systems Biology | Research | Visualization (Mental images) | Gene expression | Analysis | Proteins | Biology | Scientific imaging | Research methodology | Index Medicus
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