Pre-Prints


In an effort to increase access to our research, we are using since 2017 the biological pre-print service bioRxiv. bioRxiv is a free online archive and distribution service for unpublished preprints in the life sciences, and is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution.

Here is the list of our manuscripts deposited at bioRxiv prior to submission to a peer-reviewed journal.

8. Machine learning based prediction of functional capabilities in metagenomically assembled microbial genomes.

Fred Farrell, Orkun S Soyer, Christopher Quince
Posted April 25, 2018 | bioRxiv link

7. Synthetic methanogenic communities reveal differential impact of ecological perturbations on aceto- and hydrogeno-trophic methanogens.

Jing Chen, Matthew Wade, Jan Dolfing, Orkun S Soyer
Posted April 24, 2018 | bioRxiv link

6. Manganese oxide biomineralization is a social trait protecting against nitrite toxicity.

Christian Zerfass, Joseph A Christie-Oleza, Orkun S Soyer
Posted April 04, 2018 | bioRxiv link

5. In silico evolution of signaling networks using rule-based models: bistable response dynamics.

Song Feng, Orkun S Soyer
Posted February 06, 2018 | arxiv link

4. MetQy: an R package to query metabolic functions of genes and genomes.

Andrea Martinez-Vernon, Fred Farrell, Orkun S Soyer
Posted November 16, 2017 | bioRxiv link | Final published version @Bioinformatics, June 2018

3. Impact of spatial organization on a novel auxotrophic interaction among soil microbes.

Xue Jiang, Christian Zerfass, Ruth Eichmann, Munehiro Asally, Patrick Schaefer, Orkun Soyer
Posted September 28, 2017 | bioRxiv link | Final published version @The ISME Journal, Feb 2018

2. Integrated Human-Virus Metabolic Modelling Predicts Host-Based Antiviral Targets Against Chikungunya, Dengue and Zika Viruses.

Sean Aller, Andrew E Scott, Mitali Sarkar-Tyson, Orkun S Soyer
Posted July 19, 2017 | bioRxiv link | Resource 13 (ViraNet)

1. Predicting the structure and function of coalesced microbial communities.

Pawel Sierocinski, Kim Milferstedt, Florian Bayer, Tobias Grokopf, Mark Alston, Sarah Bastkowski, David Swarbreck, Phil J Hobbs, Orkun S Soyer, Jrme Hamelin, and Angus Buckling
Posted January 27, 2017 | bioRxiv link | Final published version @Current Biology, Sep 2017