Our People

Principal Investigator

David Umulis, Ph.D.

Dane A. Miller Head: Weldon School of Biomedical Engineering

Professor of Biomedical Engineering

Professor of Agricultural and Biological Engineering

Email: dumulis@purdue.edu

Phone: +1 765 494-1223
Fax: +1 765 496-1115

Purdue University

Weldon School of Biomedical Engineering

206 S. Martin Jischke Drive

West Lafayette, IN 47907-2032

Staff

Xiaoguang Zhu; Ph.D.

Research Scientist

Email: zhu410@purdue.edu

Research: Determine the functional significance of feedback networks in the regulation of BMP-mediated patterning by systematically evaluating gradient dynamics, robustness, and scaling of BMP signaling in wild-type and mutant zebrafish embryos, such as bambia, sizzled, and admp.]

Publications: https://www.researchgate.net/profile/Xiaoguang-Zhu-4

Linlin Li;Ph.D.

Post Doctoral Research Assistant

Email: li2212@purdue.edu

Research: Embryonic development is a complicated phenomenon that combines cellular signaling, gene regulation, and cellular movement to form structures and tissues that presage adult physiology. Morphogens mediate the cell fate decision by its time-varying spatial distribution. In zebrafish, patterns of gene expression along the dorsal-ventral (DV) body axis are regulated by Bone Morphogenetic Proteins (BMPs). In our work, we are interested in how the cellular movements impact the formation of gradients by contributing an advective term whereby the morphogens are swept with the moving cells as they move vegetally. We developed an integrated, moving-mesh Finite Element Model whereby the cell velocities directly inform the mesh movement, providing a realistic domain for computing pattern information. Our goal is to develop a complete advection-diffusion-reaction model that incorporates all stages of zebrafish embryonic development data to investigate the mechanism in underlining BMP driven DV patterning during epiboly.

Huma Shoaib; Ph.D.

Engineering Education Researcher

Profile Link: https://www.linkedin.com/in/humashoaib/

Yixuan Liu; B.S. ABE

Lab Assistant at Purdue University

Linkin Profile: https://www.linkedin.com/in/yixuan-liu-5b0092173/

Email: liu2586@purdue.edu

Responsibilities: Support and conduct experiment with Xiaoguang zhu, Linlin Li and Matthew Thompson; zebrafish house Maintenance; and provide lab support, including imaging with confocal, preparation of reagents, lab supply ordering and participate in group meetings and journal club.

Graduate Students

Matthew Thompson; Ph.D candidate

Email: thompsmj@purdue.edu

Research: The organ of Corti in the inner ear is a striking example of precise developmental patterning, where the radial pattern is faithfully repeated over 3000 times from base to apex. Each individual cell along the radial axis has a unique role, and disruption of this pattern can cause defects in hearing. I'm interested in learning how nascent cells along this axis interpret the positional information contained in transcription factor profiles before cell fate specification begins. Combining semiquantitative imaging data with tools from information theory and systems biology, I'm working on ways to decipher the complex regulatory system guiding this developmental process with an emphasis on the Bmp pathway.

Agnes Doszpoly; Ph.D student

Email: adoszpol@purdue.edu

Research Interest: Developing BTDR Fellow (Bioengineering Training in Diabetes Research), computational modeling of Type 1 Diabetes pathogenesis in zebrafish.

Nissa Jo Larson; Ph.D student

Email: larso124@purdue.edu

Research Interest: Modeling zebrafish embryo Bone Morphogenetic Protein (BMP) gradient formation, considering robustness contribution of membrane-bound BMP receptor complexes

LeRayah Neely-Brown; M.S student

Email: lneelybr@purdue.edu

Research Interest: LeRayah Neely-Brown is a first year Biomedical Engineering Master’s student. She received her BS in Mathematics and Computer Science from the University of Illinois at Chicago in 2021. Her interests lie in utilizing computational neuroscience to understand neuronal signal processing from sub-cellular to network/system-level dynamics. She aims to analyze and phenotype action potentials via biophysical and computation modeling for the vagus nerve. In her spare time, LeRayah enjoys listening to music, going to museums, and styling others’ makeup.

Alumni

Nimisha Bajaj; M.D., Ph.D.

Coadvised with Sherry Harbin and Ann Rundell

Current Position: Pediatric Resident at Nationwide Children's Hospital;

Research: Investigate the dynamics of the extracellular matrix molecules that promote and inhibit neovascularization through the mechanotransduction pathway through computational modeling and validation in vitro using a three-dimensional tissue culture system. Because the available data is largely qualitative, we are using optimal scaling and multi-objective optimization in order to fit the model parameters as well as the network structure of the experimental data.

Yan Huang; Ph.D.

Current Position: SDET at Amazon

Linkin Profile: https://www.linkedin.com/in/yanhuang1/

Research: Mechanism of scale invariance in Dorsal-Ventral patterning using quantitative imaging and mathematical modeling in zebrafish embryos.

Thembi Mdluli; Ph.D.

Coadvised with Ann Rundell

Current Position: Computational Biologist at The Henry M. Jackson Fundation for the Advancement of MIlitary Medicine

Linkin Profile: https://www.linkedin.com/in/thembi-mdluli-53829a1a/

Research: Model parameter optimization using disparate datasets is difficult because some datasets are more important or informative that others, and the tradeoff between these datasets are not clear. With multiple plausible models, models might have to sacrifice satisfaction of one dataset in order to improve the fitness of another. Multi-objective optimization searches for a set of solutions with a tradeoff between competing objectives which allows for a fair comparison between different models.

Joyatee Sarker; M.D., Ph.D.

Coadvised with Ann Rundell and Tamara Kinzer-Ursem

Current Position: Psychiatry Resident at Indiana University School of Medicine

Linkin Profile: https://www.linkedin.com/in/joyatee/

Research: Hematopoiesis within individuals differ in several ways, and Acut Myelogenous Leukemia (AML) behave differently within each patient. We have created a multi-linage computational model of the hematopoietic system, and simulated 22,796 virtual patients using unique parameter sets. Our goal is to predict the treatment schedule for individual patients' optimal recovery from leukemia.

Md. Shahriar Karim; M.S. ABE, M.S. ECE, Ph.D.

Current Position: Assistant Professor of North South University

Profile Link: http://ece.northsouth.edu/people/md-shahriar-karim/

Research Interest: Quantitative System Biology, Modeing of Dynamical Systems, Estimation and Detection Theory and Computational Biology (Cited from: http://ece.northsouth.edu/people/md-shahriar-karim/)

Michael Pargett; Ph.D.

Current Position: Project Scientist

Profile Link: https://www.mcb.ucdavis.edu/faculty-labs/albeck/aboutlab.htm

Position Description: Micheal studies how cells internally process information in signalling pathways, using signal processing and model-based computational techniques. He competed his phD at Purdue Universtiy and joined the lab at the start of 2014. ( Cited from: https://www.mcb.ucdavis.edu/faculty-labs/albeck/aboutlab.htm)

James Hengenius; Ph.D.

Current Position: Postdoc at University of Pittsburgh

Profile Link: http://huppertlab.net/people/

Joseph Zinski; Ph.D.

Co Advised with MC Mullins at Upenn

Current Position: Post Doc at Upenn

Linkin Profile: https://www.linkedin.com/in/joseph-zinski-623812a5/

Tzu-Ching Wu; Ph.D.

Current Position: PhD Candidate at Purdue Universtiy

Linkin Profile: https://www.linkedin.com/in/tzuching/

Research Website: http://tzuching1.weebly.com/

Research Fileds: Medical Image Processing, Developmental Biology, Deep Learning, Computational Biology, Multi-objective optimization (Cited from: http://tzuching1.weebly.com/)