Category: Uncategorized

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

June 1st, 2014 in Uncategorized

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 http://comets.bu.edu.

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

December 19th, 2013 in Uncategorized

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

December 19th, 2013 in Uncategorized

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

November 1st, 2013 in Uncategorized

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

September 18th, 2013 in Uncategorized

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

September 18th, 2013 in Uncategorized

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

June 5th, 2013 in Uncategorized

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

June 5th, 2013 in Uncategorized

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.