Bing Liu’s Work Published in Science Signaling

“Crosstalk Between Toll-like Receptor Pathways”Bing figure
A collaboration between the Bahar lab, the Ding lab (National Singapore University), and the Thiagarajan lab (Harvard), led by Dr. Liu in the Bahar lab.

Toll-like receptors (TLRs) recognize pathogens and stimulate the innate immune response. Liu et al uncovers how the crosstalk between TLR pathways enables macrophages to fine-tune their responses to multiple infection events. In particular, macropahges can “memorize” the first pathogen attack and boost the immune response to subsequent attacks. The crosstalk also helps to avoid the harmful excessive inflammatory responses.

Dr. Bahar participates as an invited speaker at the White House for the National Strategic Computing Initiative


A snapshot from multiscale simulations of dopamine signaling (by Cihan Kaya, in collaboration with Faeder, Sorkin, Sejnowski and Bahar labs)

Dr. Ivet Bahar was invited to participate in a workshop and give a talk at the White House for the National Strategic Computing Initiative (NSCI).

On July 29, 2015, the President issued an Executive Order creating the NSCI, a Whole-of-Nation effort to maximize the benefits of high-performance computing (HPC).

The workshop brought together 75 leaders from industry, academia, and government to discuss opportunities of HPC and solutions to the challenges faced. Dr Bahar participated in the meeting as one of the three invited speakers from academia. She presented her perspective on what is the state-of-the-art in computational biology using her NIH-funded Biomedical Technology and Research Center’s focus as a lens, and discussed current challenges that could be addressed by exascale computing through NSCI.

The title of her talk was, “Exascale Computing for Multiscale Modeling and Big Data in Biology”.

Congratulations on this wonderful opportunity!

Clark and Chikina publish their study of Marine Mammal Evolution

Clark and Chikina publish their study of Marine Mammal Evolution in Molecular Biology and Evolution. One of the authors was their former TECBio REU student, Joe Robinson. Congrats to everyone!


Mammal species have made the transition to the marine environment several times, and their lineages represent one of the classical examples of convergent evolution in morphological and physiological traits. Nevertheless, the genetic mechanisms of their phenotypic transition are poorly understood, and investigations into convergence at the molecular level have been inconclusive. While past studies have searched for convergent changes at specific amino acid sites, we propose an alternative strategy to identify those genes that experienced convergent changes in their selective pressures, visible as changes in evolutionary rate specifically in the marine lineages. We present evidence of widespread convergence at the gene level by identifying parallel shifts in evolutionary rate during three independent episodes of mammalian adaptation to the marine environment. Hundreds of genes accelerated their evolutionary rates in all three marine mammal lineages during their transition to aquatic life. These marine-accelerated genes are highly enriched for pathways that control recognized functional adaptations in marine mammals, including muscle physiology, lipid-metabolism, sensory systems, and skin and connective tissue. The accelerations resulted from both adaptive evolution as seen in skin and lung genes, and loss of function as in gustatory and olfactory genes. In regard to sensory systems, this finding provides further evidence that reduced senses of taste and smell are ubiquitous in marine mammals. Our analysis demonstrates the feasibility of identifying genes underlying convergent organism-level characteristics on a genome-wide scale and without prior knowledge of adaptations, and provides a powerful approach for investigating the physiological functions of mammalian genes.

Maria Chikina, Joe Robinson, Nathan Clark. “Hundreds of genes experienced convergent shifts in selective pressure in marine mammals.” Molecular Biology and Evolution. 2016.