Student and postdoctoral positions on microbial symbiosis in the oceans

As part of a newly funded HFSP project, we are looking for students and postdocs to join an international team to work on interactions among globally abundant marine microbes using lab and field experiments, bioinformatics analyses and genome-scale metabolic modeling. See details here.

Computation of Microbial Ecosystems in Time and Space (COMETS) paper and software available

The first paper featuring COMETS and its prediction of the dynamics of small microbial communities is out at Cell Reports. COMETS, the software, is available for download at

A new paper is out: using mathematical models to fight antibiotic resistance

Antonio Gomes’ paper “Resource competition may lead to effective treatment of antibiotic resistant infections” has been published in PLOS ONE, and is available here.

Congratulations to Sara and Lina for their successful PhD defense

Sara Baldwin Collins and Lina Faller successfully defended their Ph.D. dissertation in Bioinformatics, both presenting work on functional diversity in microbial communities. Congratulations!!!

New paper on metabolism in a microbial biofilm

Varun Mazumdar’s paper “Metabolic proximity in the order of colonization of a microbial community” has been published in PLOS ONE. The paper can be downloaded here.

Shedding light on shadow prices: flux imbalance analysis

A new PLOS Comp Bio paper by Ed Reznik, in collaboration with Pankaj Mehta, shows how the sensitivity of growth to violation of mass balance constraints in stoichiometric models can provide information on the variability of metabolite pools.

Celebrating the 100 years of Michaelis-Menten kinetics

A Special Issue of FEBS Letters is celebrating “A century of Michaelis-Menten kinetics”. We contributed to this issue with a paper titled “The average enzyme principle”. Remember the term for the enzyme concentration, E, in the Michaelis-Menten equation? What if that term becomes E(t), i.e. it depends explicitly on time, for example due to regulation? We show that, over a given time interval, the net metabolite changes depend only on the time average of E(t). The theorem can be generalized to a network of synchronously regulated reactions.

Arion Stettner’s PNAS Commentary is out

Our commentary on Flemholz et al. (“Glycolytic strategy as a tradeoff between energy yield and protein cost”) was published on PNAS

Ed Reznik wins prize for best Ph.D. dissertation in BME

Congratulation to Dr. Ed Reznik for graduating in BME, and winning a prize for best Ph.D. dissertation.

Check Ed’s latest work on enzyme regulationmetabolic-genetic oscillators, and transcription-FBA integration.