Institution
Biomax Informatics AG
Company•Munich, Germany•
About: Biomax Informatics AG is a company organization based out in Munich, Germany. It is known for research contribution in the topics: Systems medicine & Asthma. The organization has 43 authors who have published 85 publications receiving 4448 citations.
Topics: Systems medicine, Asthma, Knowledge base, Genome, Health care
Papers published on a yearly basis
Papers
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DSM1, Delft University of Technology2, University of Nottingham3, Technical University of Denmark4, Wageningen University and Research Centre5, University of Sheffield6, Utrecht University7, Biomax Informatics AG8, CLC bio9, University of Liverpool10, Ghent University11, University of Manchester12, University of Provence13, University of Groningen14, Pasteur Institute15, University of Amsterdam16, University of Angers17, Leiden University18, Radboud University Nijmegen19, University of Szeged20
TL;DR: The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid, and the sequenced genome revealed a large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors.
Abstract: The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.
1,161 citations
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TL;DR: Genes predicted to encode transporters were strongly overrepresented among the genes transcriptionally upregulated under conditions that stimulate penicillinG production, illustrating potential for future genomics-driven metabolic engineering.
Abstract: Industrial penicillin production with the filamentous fungus Penicillium chrysogenum is based on an unprecedented effort in microbial strain improvement. To gain more insight into penicillin synthesis, we sequenced the 32.19 Mb genome of P. chrysogenum Wisconsin54-1255 and identified numerous genes responsible for key steps in penicillin production. DNA microarrays were used to compare the transcriptomes of the sequenced strain and a penicillinG high-producing strain, grown in the presence and absence of the side-chain precursor phenylacetic acid. Transcription of genes involved in biosynthesis of valine, cysteine and alpha-aminoadipic acid-precursors for penicillin biosynthesis-as well as of genes encoding microbody proteins, was increased in the high-producing strain. Some gene products were shown to be directly controlling beta-lactam output. Many key cellular transport processes involving penicillins and intermediates remain to be characterized at the molecular level. Genes predicted to encode transporters were strongly overrepresented among the genes transcriptionally upregulated under conditions that stimulate penicillinG production, illustrating potential for future genomics-driven metabolic engineering.
457 citations
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TL;DR: Analysis of virulence-associated traits expressed in the two UPEC O6 strains, together with genome comparison, demonstrate the marked genetic and phenotypic variability among UPEC.
Abstract: Uropathogenic Escherichia coli (UPEC) strain 536 (O6:K15:H31) is one of the model organisms of extraintestinal pathogenic E. coli (ExPEC). To analyze this strain's genetic basis of urovirulence, we sequenced the entire genome and compared the data with the genome sequence of UPEC strain CFT073 (O6:K2:H1) and to the available genomes of nonpathogenic E. coli strain MG1655 (K-12) and enterohemorrhagic E. coli. The genome of strain 536 is approximately 292 kb smaller than that of strain CFT073. Genomic differences between both UPEC are mainly restricted to large pathogenicity islands, parts of which are unique to strain 536 or CFT073. Genome comparison underlines that repeated insertions and deletions in certain parts of the genome contribute to genome evolution. Furthermore, 427 and 432 genes are only present in strain 536 or in both UPEC, respectively. The majority of the latter genes is encoded within smaller horizontally acquired DNA regions scattered all over the genome. Several of these genes are involved in increasing the pathogens' fitness and adaptability. Analysis of virulence-associated traits expressed in the two UPEC O6 strains, together with genome comparison, demonstrate the marked genetic and phenotypic variability among UPEC. The ability to accumulate and express a variety of virulence-associated genes distinguishes ExPEC from many commensals and forms the basis for the individual virulence potential of ExPEC. Accordingly, instead of a common virulence mechanism, different ways exist among ExPEC to cause disease.
353 citations
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TL;DR: A web-survey is used to assess current research projects on data-integration to tap into the views, needs and challenges as currently perceived by parts of the research community.
Abstract: To integrate heterogeneous and large omics data constitutes not only a conceptual challenge but a practical hurdle in the daily analysis of omics data. With the rise of novel omics technologies and through large-scale consortia projects, biological systems are being further investigated at an unprecedented scale generating heterogeneous and often large data sets. These data-sets encourage researchers to develop novel data integration methodologies. In this introduction we review the definition and characterize current efforts on data integration in the life sciences. We have used a web-survey to assess current research projects on data-integration to tap into the views, needs and challenges as currently perceived by parts of the research community.
348 citations
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Technical University of Denmark1, DSM2, Pacific Northwest National Laboratory3, Biomax Informatics AG4, Novozymes5, University of Göttingen6, University of Seville7, Concordia University8, Chr. Hansen9, United States Department of Energy10, Stanford University11, Vienna University of Technology12, Los Alamos National Laboratory13
TL;DR: In this article, the authors performed whole-genome sequencing of the Aspergillus niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality.
Abstract: The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.
308 citations
Authors
Showing all 43 results
Name | H-index | Papers | Citations |
---|---|---|---|
Dieter Maier | 27 | 69 | 3213 |
Angela Bauch | 13 | 27 | 6871 |
Kaj Albermann | 12 | 19 | 4702 |
Christian Wagner | 9 | 20 | 1186 |
Klaus Heumann | 8 | 14 | 507 |
Sascha Losko | 6 | 10 | 153 |
Richard Albang | 6 | 15 | 2123 |
Markus Butz-Ostendorf | 5 | 11 | 77 |
Beatrix Gerhard | 4 | 6 | 126 |
Andreas Kaps | 4 | 7 | 517 |
Andreas Fritz | 3 | 7 | 63 |
Wenzel Kalus | 3 | 3 | 76 |
Andreas Volz | 3 | 3 | 309 |
Philipp Krubasik | 2 | 5 | 14 |
Sebastian J. Kopetzky | 2 | 3 | 41 |