112 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- Massachusetts Institute of TechnologyUS8 papers
- Harvard UniversityUS4 papers
- Centre National de la Recherche ScientifiqueFR2 papers
- Biologie Computationnelle, Quantitative et SynthétiqueFR1 paper
- Brigham and Women's HospitalUS1 paper
- Broad InstituteUS1 paper
- Consejo Superior de Investigaciones CientíficasES1 paper
- École Normale Supérieure - PSLFR1 paper
- Heidelberg Institute for Theoretical StudiesDE1 paper
- Heidelberg UniversityDE1 paper
- Helmholtz MunichDE1 paper
- IIT@MITUS1 paper
10 papers
Nano-engineered surface enhanced Raman spectroscopy substrates for probing tissue-material interactions
Connie M. Wang, Roberta M. Sabino, Aditya Garg +3
Innovation in biomaterials has brought both breakthroughs and new challenges in medicine, as implant materials have become increasingly multifunctional and complex. One of the grea…
The Human Cell Atlas & Equity: Lessons Learned
Partha P. Majumder, Musa M. Mhlanga, Alex K. Shalek
The Human Cell Atlas has been undergoing a massive effort to support global scientific equity. The co-leaders of its Equity Working Group share some lessons learned in the process.
PEtab -- interoperable specification of parameter estimation problems in systems biology
Leonard Schmiester, Yannik Schälte, Frank T. Bergmann +26
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of p…
Large-scale inference of correlation among mixed-type biological traits with phylogenetic multivariate probit models
Zhenyu Zhang, Akihiko Nishimura, Paul Bastide +5
Inferring concerted changes among biological traits along an evolutionary history remains an important yet challenging problem. Besides adjusting for spurious correlation induced f…
On the entropy of protein families
John Barton, Arup Chakraborty, Simona Cocco +2
Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The…
Identification of drug resistance mutations in HIV from constraints on natural evolution
Thomas C. Butler, John P. Barton, Mehran Kardar +1
Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we sh…
Large Pseudo-Counts and -Norm Penalties Are Necessary for the Mean-Field Inference of Ising and Potts Models
J. P. Barton, S. Cocco, E. De Leonardis +1
Mean field (MF) approximation offers a simple, fast way to infer direct interactions between elements in a network of correlated variables, a common, computationally challenging pr…
Spin models inferred from patient data faithfully describe HIV fitness landscapes and enable rational vaccine design
Karthik Shekhar, Claire F. Ruberman, Andrew L. Ferguson +3
Mutational escape from vaccine induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Kno…
The energy costs of biological insulators
John Barton, Eduardo D. Sontag
Biochemical signaling pathways can be insulated from impedance and competition effects through enzymatic "futile cycles" which consume energy, typically in the form of ATP. We hypo…
The influence of T cell development on pathogen specificity and autoreactivity
Andrej Kosmrlj, Mehran Kardar, Arup K. Chakraborty
T cells orchestrate adaptive immune responses upon activation. T cell activation requires sufficiently strong binding of T cell receptors on their surface to short peptides derived…