MMBioS Cell Modeling Workshop: May 4 – May 7, 2020

We are proud to announce our latest workshop:

Dates: May 4 – May 7, 2020
Application deadline: March 6, 2020

Location: La Jolla, CA

For more details, or to apply visit:

The Cell Modeling workshop will cover theory and practice for the design and simulation of cell models focused on diffusion-reaction systems such as neurotransmission, signaling cascades, and other forms of biochemical networks. During the workshop, participants will learn how to use the tools developed by MMBioS to create, run, and analyze models of cellular microphysiology and apply them to their own research questions. In particular, the workshop will focus on:

  1. The latest version of the MCell simulation environment, including new Monte Carlo methods for 3-D simulation of reactions in solution and on arbitrarily shaped biological surfaces.
  2. Novel tools to construct and simulate rule-based models using the BioNetGen software
  3. The CellOrganizer system for creating image-derived models of cell shape and intracellular organization that can be used to compare cell populations and as the basis for cell simulations
  4. The newest version of CellBlender, our MCell model creation and visualization framework. The attendees are encouraged to bring ideas/data for their own simulation projects.

Robin E.C. Lee Named Sloan Foundation Research Fellow

Robin E.C. Lee, Assistant Professor in the Department of Computational & Systems Biology, has been named one of the 126 Sloan Research Fellows for 2020.

“To receive a Sloan Research Fellowship is to be told by your fellow scientists that you stand out among your peers,” says Adam F. Falk, president of the Alfred P. Sloan Foundation. “A Sloan Research Fellow is someone whose drive, creativity, and insight makes them a researcher to watch.”

Fellows from the 2020 cohort are drawn from a diverse range of more than 60 institutions across the U.S. and Canada, “There is a wide variety of winning institutions, but each one has successfully attracted, retained, and nurtured truly promising junior faculty,” says Daniel L. Goroff, director of the Sloan Research Fellowship program. “The Alfred P. Sloan Foundation is proud to join with these institutions in recognizing and supporting scientific leaders of the future.”

Open to scholars in eight scientific and technical fields—chemistry, computer science, economics, mathematics, computational and evolutionary molecular biology, neuroscience, ocean sciences, and physics—the Sloan Research Fellowships are awarded in close coordination with the scientific community. Candidates must be nominated by their fellow scientists and winners are selected by independent panels of senior scholars on the basis of a candidate’s research accomplishments, creativity, and potential to become a leader in his or her field.

Carvunis Lab Publish in Nature Communications

De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences

Recent evidence demonstrates that novel protein-coding genes can arise de novo from nongenic loci. This evolutionary innovation is thought to be facilitated by the pervasive translation of non-genic transcripts, which exposes a reservoir of variable polypeptides to natural selection. We find that adaptive emerging sequences tend to encode putative transmembrane domains, and that thymine-rich intergenic regions harbor a widespread potential to produce transmembrane domains. These findings, together with in-depth examination of the de novo emerging YBR196C-A locus, suggest a novel evolutionary model whereby adaptive transmembrane polypeptides emerge de novo from thymine-rich nongenic regions and subsequently accumulate changes molded by natural selection.



Vakirlis N, Acar O, Hsu B, Coelho NC, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman II RW, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O’Donnell AF, Ideker T, Carvunis AR. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat Commun 11, 781 (2020).

Robin Lee, Rachel Gottschalk, and Agustin Cruz Awarded AAI Intersect Fellowship

Robin Lee (left), Agustin Cruz (center), Rachel Gottschalk (right)

The American Association of Immunologists(AAI) awarded Drs. J. Agustin Cruz and Robin E.C. Lee the Intersect Fellowship 2020. Dr. Cruz holds a PhD in Immunology and has been working for the past two years as a postdoctoral associate with Dr. Lee to decode intracellular mechanisms of information transmission in response to changing extracellular environments. This AAI intersect fellowship aims to support Dr. Cruz’s postdoctoral training in computational biology while he studies the dynamics of immunological inflammatory signaling pathways in human-derived macrophages and cancer cell lines. This is a project in collaboration with Dr. Rachel Gottschalk from the Department of Immunology. In this new collaborative project, Dr. Cruz will dissect the physical and temporal features of key intermediate proteins of the nuclear-factor kappa-B (NF-KB) and the mitogen-activated kinase (MAPK) signaling pathways and relate the features of these pathways to cell fate decisions.

James Krieger received the DCSB Best Postdoctoral Associate Award of the Year 2019

Dr. James Krieger received the DCSB Best Postdoctoral Associate Award of the Year 2019. He was nominated by his mentor, Dr. Ivet Bahar. Over the past year, he has contributed to 6 articles listed below.  James is the one of three first authors in a seminal paper on the signature dynamics of proteins, Shared signature dynamics tempered by local fluctuations enables fold adaptability and specificity, published in Mol Biol Evol. He made a major contribution to this study in which he demonstrated the existence of a dynamics signature shared by the members of each protein family, and how the signature dynamics differentiates to enable functional specificity among family members. James will be leaving the University of Pittsburgh in March 2020 for the next step in his career, to work on modeling the structure and dynamics of cryo-EM resolved biological assemblies as a Research Scientist at the University of Madrid, Spain. We wish James the best in his new position and thank him for all of his valuable contributions.


  1. Lee JY, Krieger JM, Li H, Bahar I. (2019) Pharmmaker: Pharmacophore Modeling and Hit Identification Based on Druggability Simulations.Protein Sci, 29(1):76-86. PMID: 31576621 PMCID:6933858
  2. Zhang S,* Li H,* Krieger JM,*Bahar I. (2019) Shared signature dynamics tempered by local fluctuations enables fold adaptability and specificityMol Biol Evol 36: 2053-2068. PMID: 31028708 PMCID: 6736388
  3. Mikulska-Ruminska K, Shrivastava IH, Krieger JM, Zhang S, Li H, Bayir H, Wenzel SE, VanDemark AP, Kagan VE, Bahar I.(2019) Characterization of differential dynamics, specificity, and allostery of lipoxygenase family membersJ Chem Inf Model 59: 2496-2508. PMID: 30762363 PMCID: 6541894
  4. COS Sorzano, A Jiménez, J Mota, JL Vilas, D Maluenda, M Martínez, E Ramírez-Aportela, T Majtner, J Segura, R Sánchez-García, Y Rancel, L del Caño, P Conesa, R Melero, S Jonic, J Vargas, F Cazals, Z Freyberg, JM Krieger,I Bahar, R Marabini, JM Carazo (2019) Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy. Acta Crystallog F Struct Biol Commun 75: 19-32. PMID: 30605122 PMCID: 6317454
  5.  Lee JY, Krieger JM, Herguedas B, García-Nafría J, Dutta A, Shaikh SA, Greger IH, Bahar I. (2019) Druggability Simulations and X-ray Crystallography Reveal a Ligand-binding Site in the GluA3 AMPA Receptor N-terminal Domain.Structure 27: 241-252. PMID: 30528594 PMCID: 6365164
  6. Zhang Y., Doruker P., Kaynak B., Zhang S, Krieger JM, Li, H & Bahar I. (2019)  Intrinsic dynamics is evolutionarily optimized to enable allosteric behaviorCurr Opin Struct Biol, 62:14-21 PMID: 31785465