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.
We attended the ISMB 2018 conference of the ISCB (International Society of Computational Biology) from July 6 to July 10 at Chicago.
Yannick gave a talk titled HFSP: High speed homology-driven function annotation of proteins.
Chengsheng gave a talk titled mi-faser deciphers city subway microbiome functional fingerprints.
Max gave a talk titled Identifying protein positions for variation driven functional tuning.
Yanran gave a talk titled Identifying Crohn’s disease signal from variome analysis.
HFSP: high speed homology-driven function annotation of proteins Yannick Mahlich, Martin Steinegger, Burkhard Rost, Yana Bromberg
Bioinformatics, Volume 34, Issue 13, 1 July 2018, Pages i304–i312 https://doi.org/10.1093/bioinformatics/bty262
The rapid drop in sequencing costs has produced many more (predicted) protein sequences than can feasibly be functionally annotated with wet-lab experiments. Thus, many computational methods have been developed for this purpose. Most of these methods employ homology-based inference, approximated via sequence alignments, to transfer functional annotations between proteins.
mi-faser: major update of web-service and standalone-version New in the public web-service:
NMDS analysis between submitted samples
Register user account for faster access to submissions / analyses
faster submission processing (less then ~15min per 20GB reads)
Batch submissions (up to 100 input files)
Paired-end input processing
Quality-Control pipeline for fastq input
New in the standalone-version:
threaded processing (split input files and process in parallel)
built-in up/downgrade to diamond version of choice
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.
Dr. Yana Bromberg is chairing the Proteins session of the fourth International Society for Computational Biology Latin America Bioinformatics Conference (ISCB-LA) together with Dr. Diego U. Ferreiro (Laboratorio de Fisiología de Proteins, Dpto Química Biológica / IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires).