Functional sequencing read annotation for high precision microbiome analysis
Chengsheng Zhu, Maximilian Miller, Srinayani Marpaka, Pavel Vaysberg, Malte C. Rühlemann, Guojun Wu Femke-Anouska Heinsen, Marie Tempel, Liping Zhao, Wolfgang Lieb Andre Franke, Yana Bromberg. Nucleic Acids Research, https://doi.org/10.1093/nar/gkx1209
The mi-faser microbiome analysis pipeline, combining faser with our manually curated reference database of protein functions, accurately annotates microbiome molecular functionality. mi-faser’s minutes-per-microbiome processing speed is significantly faster than that of other methods, allowing for large scale comparisons.
Here, we identified previously unseen oil degradation-specific functions in BP oil-spill data, as well as functional signatures of individual-specific gut microbiome responses to a dietary intervention in children with Prader–Willi syndrome. Our method also revealed variability in Crohn's Disease patient microbiomes and clearly distinguished them from those of related healthy individuals. Our analysis highlighted the microbiome role in CD pathogenicity, demonstrating enrichment of patient microbiomes in functions that promote inflammation and that help bacteria survive it.
fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks
Zhu Chengsheng, Mahlich Yannick, Miller Maximilian, Bromberg Yana; fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks, Nucleic Acids Research, https://doi.org/10.1093/nar/gkx1060
We describe fusionDB, a novel database that uses our functional data to represent 1374 taxonomically distinct bacteria annotated with available metadata: habitat/niche, preferred temperature, and oxygen use. Each microbe is encoded as a set of functions represented by its proteome and individual microbes are connected via common functions.
Users can search fusionDB via combinations of organism names and metadata. Moreover, the web interface allows mapping new microbial genomes to the functional spectrum of reference bacteria, rendering interactive similarity networks that highlight shared functionality. fusionDB provides a fast means of comparing microbes, identifying potential horizontal gene transfer events, and highlighting key environment-specific functionality.
We developed clubber (CLUster-load Balancer for Bioinformatics E-Resources) to automate distribution of computation between independent and heterogenous compute resources based on individual workloads, queueing, and computation times.
Publication: JIB, https://doi.org/10.1515/jib-2017-0020
A paper came out in Nature Scientific Reports with collaborators Jonas Reeb, Maximilian Hecht, Maria Schelling, Tjaart Andries Petrus De Beer, Yana Bromberg & Burkhard Rost.
The title of the paper is "Common sequence variants affect molecular function more than rare variants?"
A paper came out in Human mutation, variation, informatics and desease, with collaborators Marco Carraro, Giovanni Minervini, Manuel Giollo, Emidio Capriotti, Rita Casadio, Roland Dunbrack, Lisa Elefanti, Pietro Fariselli, Carlo Ferrari, Julian Gough, Panagiotis Katsonis, Emanuela Leonardi, Olivier Lichtarge, Chiara Menin, Pier Luigi Martelli, Abhishek Niroula, Lipika R. Pal, Susanna Repo, Maria Chiara Scaini, Mauno Vihinen, Qiong Wei, Qifang Xu, Yuedong Yang, Yizhou Yin, Jan Zaucha, Huiying Zhao, Yaoqi Zhou, Steven E. Brenner, John Moult, and Silvio C.E. Tosatto.
The name of the paper is "Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI".