Bromberg Lab Attended ISMB 2018


The Bromberg lab attend 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.

Zishuo presented a poster titled A survey of synonymous single nucleotide variants reveals preference for specific codons and amino acids.








Chengsheng Won the Best Talk for CAMDA challenge in ISMB 2018

Congratulations to Chengsheng, who won the Best Talk prize on July 8 for the CAMDA (Critical Assessment of Massive Data Analysis) challenge during the ISMB 2018 conference of the ISCB (International Society of Computational Biology).




New Publication by Yannick Mahlich and Others

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


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. The increase in the number of available sequences, however, has drastically increased the search space, thus significantly slowing down alignment methods.Here we describe homology-derived functional similarity of proteins (HFSP), a novel computational method that uses results of a high-speed alignment algorithm, MMseqs2, to infer functional similarity of proteins on the basis of their alignment length and sequence identity. We show that our method is accurate (85% precision) and fast (more than 40-fold speed increase over state-of-the-art). HFSP can help correct at least a 16% error in legacy curations, even for a resource of as high quality as Swiss-Prot. These findings suggest HFSP as an ideal resource for large-scale functional annotation efforts.



Services updated

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

  • user-interface updates


New in the standalone-version:

  • threaded processing (split input files and process in parallel)

  • built-in up/downgrade to diamond version of choice

sourcecode available (

download latest release ( (10.21 MB)

New Publication by Chengsheng Zhu and others

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

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.



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 Research

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.