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

Weikang Wang wins DCSB Best Postdoc of the Year Award for 2019 at the CSB Annual Appreciation lunch

Jianhua Xing (left) and Weikang Wang (right)

Dr. Weikang Wang received the DCSB Best Postdoctoral Associate Award of the Year 2019. He was nominated by his mentor, Dr. Jianhua Xing. Dr. Wang tackled a very challenging problem of how to extract dynamical information from single cell studies. He established an experimental/computational framework, and introduced techniques from microscopy, machine learning,  nonlinear and chemical physics for quantitative studies of cell phenoytpic transition dynamics, as exampled by the manuscripts below.

1) Weikang Wang, David A. Taft, Yijiun Chen, Jingyu Zhang, Callen Wallace, Min Xu, Simon C. Watkins, Jianhua Xing, Learn to segment single cells with deep distance estimator and deep cell detector. Computers in Biology and Medicine, 108: 133-141 (2019).

2) Weikang Wang and Jianhua Xing, Analyses of Multi-dimensional Single Cell Trajectories Quantify Transition Paths between Nonequilibrium Steady States, BioRxiv copy, submitted.

3)  Weikang Wang, Diana L. Douglas, Jingyu Zhang, Yi-Jiun Chen, Ya-Yun Cheng, Sangeeta Kumari, Metewo Selase Enuameh, Yan Dai, Callen T. Wallace, Simon C. Watkins, Weiguo Shu, Jianhua Xing, M-TRACK: a platform for live cell multiplex imaging reveals cell phenotypic transition dynamics inherently missing in snapshot data, BioRxiv copy, submitted.

Sanjana Gupta received the DCSB Best Student of the Year Award for 2019 at the CSB Annual Appreciation lunch

Sanjana here with her co-advisors, Dr. James R. Faeder (l) and Dr. Robin E.C. Lee (r).

Sanjana Gupta received the DCSB Best PhD Student of the Year Award for 2019 at the CSB Annual Appreciation lunch held at the University Club on Pitt’s Oakland campus, December 4, 2019. She was nominated by her co-advisors, Dr. James R. Faeder and Dr. Robin E.C. Lee for her current work on addressing the question of parameterization of mechanistic models of signal transduction. Sanjana has developed an approach based on Lasso regularization commonly used in genomics to fitting mechanistic models in order to obtain reduced or parsimonious models that describe cellular responses under specific conditions. An abstract describing this work was accepted for a talk at the recent Q-bio Conference and her presentation there was very well-received. Several members of the science community contacted both Jim and Robin to express their enthusiasm with Sanjana’s presentation and current research. A pre-print of this work is available on bioRxiv, Parallel Tempering with Lasso for Model Reduction in Systems Biology. A manuscript of that preprint is under revision with PloS Computational Biology. Overall, Sanjana has made outstanding progress in her research during the previous year and is poised to publish several papers in the beginning of 2020 that will have a strong impact on the entire systems biology community. Congratulations Sanjana!

Koes Lab Members Win NCATS ASPIRE Challenge

(left to right) Paul Francoeur, Jonathan King, David Koes, Jocelyn Sunseri, Matthew Ragoza

Dr. Koes and his lab members were among the winners of the NCATS ASPIRE 2018 Award for the following project:

Deep and Generative Structure-Based Models for Drug Discovery

Dr. David Koes
Dr. Matthew Ragoza
Jocelyn Sunseri
Paul Francoeur
Jonathan King

The project team proposes to make open source tools and resources available to researchers that enable the rapid identification and optimization of small molecule therapeutics for structure-enabled molecular targets for pain and opioid abuse.

The goal of the 2018 NCATS ASPIRE Design Challenges is to generate innovative and catalytic approaches toward solving the opioid crisis through the development of next-generation addiction-free analgesics with new chemistries, data-mining and analytical tools and technologies, as well as biological assays that will revolutionize discovery, development and pre-clinical testing of new and safer treatments for pain, opioid use disorder (OUD) and overdose.