Martin Liepach - Academia.edu (original) (raw)
Papers by Martin Liepach
Brill | Schöningh eBooks, Jun 2, 2023
Göttingen: V&R unipress, Apr 1, 2014
The High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity an... more The High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity and evolutionary hotspot. Lichens, which are complex symbiotic structures that contain diverse commensal microbial communities, are prevalent in Paramos. There they play vital roles in soil formation and mineral fixation. In this study we analyzed the microbiomes of seven lichen genera in two Colombian Paramos using 16S rRNA gene analyses and provide the first description of the bacterial communities associated with Cora and Hypotrachyna lichens. Paramo lichen microbiomes were diverse, and in some cases were distinguished based on the identity of the lichen host. The majority of the lichen-associated microorganisms were not present in all lichens sampled and could be considered transient or specialists. We also uncovered sixteen shared taxa that suggest a core lichen microbiome among this diverse group of lichens, broadening our concept of these symbiotic structures. Additionally, we ident...
We have created a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 citie... more We have created a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities across 3 years. This is the first systematic, worldwide study cataloging the urban microbial ecosystem. We identify taxonomically-defined microorganisms collected across three years. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics AMR markers, and novel genetic elements, including 10,928 viral, 1302 bacteria, and 2 archaea novel species. We identify 4,424 species of urban microorganisms and a consistent “core” of 31 species found in nearly all samples that is largely distinct from any human commensal microbiome. Profiles of AMR genes show geographic variation in type and density. Together, these results constitute a high-resolution, global metagenomic atlas, which enables the discovery of new genetic components, highlights potential forensic applications, and provides an essential first draft of the global AMR burden of the world’s ...
Genome Research, 2018
Emerging Linked-Read technologies (aka read cloud or barcoded short-reads) have revived interest ... more Emerging Linked-Read technologies (aka read cloud or barcoded short-reads) have revived interest in short-read technology as a viable approach to understand large-scale structures in genomes and metagenomes. Linked-Read technologies, such as the 10x Chromium system, use a microfluidic system and a specialized set of 3′ barcodes (aka UIDs) to tag short DNA reads sourced from the same long fragment of DNA; subsequently, the tagged reads are sequenced on standard short-read platforms. This approach results in interesting compromises. Each long fragment of DNA is only sparsely covered by reads, no information about the ordering of reads from the same fragment is preserved, and 3′ barcodes match reads from roughly 2–20 long fragments of DNA. However, compared to long-read technologies, the cost per base to sequence is far lower, far less input DNA is required, and the per base error rate is that of Illumina short-reads. In this paper, we formally describe a particular algorithmic issue c...
Genome Biology, 2017
Background: One of the main challenges in metagenomics is the identification of microorganisms in... more Background: One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited. Results: In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers. Tools were characterized on the basis of their ability to identify taxa at the genus, species, and strain levels, quantify relative abundances of taxa, and classify individual reads to the species level. Strikingly, the number of species identified by the 11 tools can differ by over three orders of magnitude on the same datasets. Various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species. Overall, pairing tools with different classification strategies (k-mer, alignment, marker) can combine their respective advantages. Conclusions: This study provides positive and negative controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results.
Historische Zeitschrift, 2015
Historische Zeitschrift, 2014
In Weimar Germany various discussions and at tempts were started to build up a democratic-liberal... more In Weimar Germany various discussions and at tempts were started to build up a democratic-liberal mass party. In 1930 the German State Party was constituted by former Democrats (DDP) and the Young German Order. The new party irritated several sections and provincial branches of the DDP and caused disaffection. Some critics founded the Independent Democratic League and subse quently the Radical Democratic Party (Radikal-Demokra tische Partei). In November 1931 this party ran for election the first time in Hesse-Darmstadt. The outcome was disap pointing. The party failed and did not gain a seat. This study describes the political fractions which supported the Radical Democratic Party and analyses by means of quanti tative methods the failures of the party. Gescheiterte Parteineugr?ndungen fallen in der Regel alsbald den Fu?noten der Geschichtsschreibung anheim. Der me?bare Erfolg von Parteien liefert die Le gitimation f?r bedeutsame Abhandlungen. Doch l??t sich annehmen, da? die Hoffn...
Historical Social Research, 1997
German Jews adopted many principles of Liberalism and generally it is taken as a fact that most J... more German Jews adopted many principles of Liberalism and generally it is taken as a fact that most Jews voted for the liberal parties and supported constitutional government. But what extent had this electoral support? Is there any difference between Left and Right wing Liberalism? How strong were the links when liberal parties disappeared from the political scene during the last years of the Weimar Republic? According to various authors there is evidence that there had been a shift of Jewish voters during the final years of the republic to the Social Democrats, others claim an increasing amount of votes for the Centre Party or refer to a continuing support of Liberalism. The hypothesis differ widely and without further empirical or theoretical evidence, it is simply a matter of conviction which theory one prefers. This study establishes by means of quantitative methods the influence of the Jewish population on the sucess of the various parties in the rural areas of Baden in the Reichs...
Brill | Schöningh eBooks, Jun 2, 2023
Göttingen: V&R unipress, Apr 1, 2014
The High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity an... more The High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity and evolutionary hotspot. Lichens, which are complex symbiotic structures that contain diverse commensal microbial communities, are prevalent in Paramos. There they play vital roles in soil formation and mineral fixation. In this study we analyzed the microbiomes of seven lichen genera in two Colombian Paramos using 16S rRNA gene analyses and provide the first description of the bacterial communities associated with Cora and Hypotrachyna lichens. Paramo lichen microbiomes were diverse, and in some cases were distinguished based on the identity of the lichen host. The majority of the lichen-associated microorganisms were not present in all lichens sampled and could be considered transient or specialists. We also uncovered sixteen shared taxa that suggest a core lichen microbiome among this diverse group of lichens, broadening our concept of these symbiotic structures. Additionally, we ident...
We have created a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 citie... more We have created a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities across 3 years. This is the first systematic, worldwide study cataloging the urban microbial ecosystem. We identify taxonomically-defined microorganisms collected across three years. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics AMR markers, and novel genetic elements, including 10,928 viral, 1302 bacteria, and 2 archaea novel species. We identify 4,424 species of urban microorganisms and a consistent “core” of 31 species found in nearly all samples that is largely distinct from any human commensal microbiome. Profiles of AMR genes show geographic variation in type and density. Together, these results constitute a high-resolution, global metagenomic atlas, which enables the discovery of new genetic components, highlights potential forensic applications, and provides an essential first draft of the global AMR burden of the world’s ...
Genome Research, 2018
Emerging Linked-Read technologies (aka read cloud or barcoded short-reads) have revived interest ... more Emerging Linked-Read technologies (aka read cloud or barcoded short-reads) have revived interest in short-read technology as a viable approach to understand large-scale structures in genomes and metagenomes. Linked-Read technologies, such as the 10x Chromium system, use a microfluidic system and a specialized set of 3′ barcodes (aka UIDs) to tag short DNA reads sourced from the same long fragment of DNA; subsequently, the tagged reads are sequenced on standard short-read platforms. This approach results in interesting compromises. Each long fragment of DNA is only sparsely covered by reads, no information about the ordering of reads from the same fragment is preserved, and 3′ barcodes match reads from roughly 2–20 long fragments of DNA. However, compared to long-read technologies, the cost per base to sequence is far lower, far less input DNA is required, and the per base error rate is that of Illumina short-reads. In this paper, we formally describe a particular algorithmic issue c...
Genome Biology, 2017
Background: One of the main challenges in metagenomics is the identification of microorganisms in... more Background: One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited. Results: In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers. Tools were characterized on the basis of their ability to identify taxa at the genus, species, and strain levels, quantify relative abundances of taxa, and classify individual reads to the species level. Strikingly, the number of species identified by the 11 tools can differ by over three orders of magnitude on the same datasets. Various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species. Overall, pairing tools with different classification strategies (k-mer, alignment, marker) can combine their respective advantages. Conclusions: This study provides positive and negative controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results.
Historische Zeitschrift, 2015
Historische Zeitschrift, 2014
In Weimar Germany various discussions and at tempts were started to build up a democratic-liberal... more In Weimar Germany various discussions and at tempts were started to build up a democratic-liberal mass party. In 1930 the German State Party was constituted by former Democrats (DDP) and the Young German Order. The new party irritated several sections and provincial branches of the DDP and caused disaffection. Some critics founded the Independent Democratic League and subse quently the Radical Democratic Party (Radikal-Demokra tische Partei). In November 1931 this party ran for election the first time in Hesse-Darmstadt. The outcome was disap pointing. The party failed and did not gain a seat. This study describes the political fractions which supported the Radical Democratic Party and analyses by means of quanti tative methods the failures of the party. Gescheiterte Parteineugr?ndungen fallen in der Regel alsbald den Fu?noten der Geschichtsschreibung anheim. Der me?bare Erfolg von Parteien liefert die Le gitimation f?r bedeutsame Abhandlungen. Doch l??t sich annehmen, da? die Hoffn...
Historical Social Research, 1997
German Jews adopted many principles of Liberalism and generally it is taken as a fact that most J... more German Jews adopted many principles of Liberalism and generally it is taken as a fact that most Jews voted for the liberal parties and supported constitutional government. But what extent had this electoral support? Is there any difference between Left and Right wing Liberalism? How strong were the links when liberal parties disappeared from the political scene during the last years of the Weimar Republic? According to various authors there is evidence that there had been a shift of Jewish voters during the final years of the republic to the Social Democrats, others claim an increasing amount of votes for the Centre Party or refer to a continuing support of Liberalism. The hypothesis differ widely and without further empirical or theoretical evidence, it is simply a matter of conviction which theory one prefers. This study establishes by means of quantitative methods the influence of the Jewish population on the sucess of the various parties in the rural areas of Baden in the Reichs...