News

New Publication by Chengsheng Zhu and others

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 Researchhttps://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.

paper

New Publication by Yana Bromberg

Figure from the new paper    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".