The Research Group of Suzanne Sindi focuses on theoretical and computational modeling of biological phenomena. Specifically, we are interested in the following:

- Dynamics and Transmission of Prion Proteins in Yeast
- Identification of Structural Variation from High Throughput Sequencing Data
- Genome Evolution and Population Dynamics

**Graduate Student and Postdoctoral Positions Available:**

Professor Sindi is currently accepting applications for graduate students and postdoctoral researchers. Desired background is in applied mathematics, specifically mathematical biology, with experience in scientific computing. Interested candidates should send a CV and cover letter to Dr. Sindi.

### Recent News:

- November 15, 2016: Book Chapter: "Mathematical Modeling of
*in vivo*Prion Disease Dynamics" to appear in the book Prion, ISBN 978-953-51-5046-6. - October 21, 2016: Mr. Michael Stobb passes his Qualifying Exam! Congratulations and thanks to Co-Advisor Prof. Karin Leiderman (School of Mines) and my colleagues Prof. Noemi Petra and Prof. Harish Bhat for serving on his committee.
- October 19, 2016: Collaborative work with Serio Lab accepted to PLoS Genetics! Congratulations to all, but especially Dr. Christine Langolis as this bulk of this work was from her Thesis.
- September 8, 2016: NSF Graduate Training Grant Awarded to UC Merced! (Stay tuned for more awesome news...)
- September 6, 2016: Mr. Mario Banuelos passes his Qualifying Exam! Congratulations on advancing to candidacy Mario and thanks to my wonderful colleagues Prof Arnold Kim and Prof Roummel Marcia for serving on his committee.
- August 18, 2016: Behavioral research paper published! Congratulations to Jason Davis and Dave Vinson (Cog Sci) as well as Prof Rick Dale!
- August 2016: REU and UROC undergraduate researchers present at the Annual UC Merced Undergraduate Research Symposium!
- May 19-20 2016: CoPIs Prof Suzanne Sindi, Applied Mathematics and Prof Jennifer Manilay host Interdisciplinary Workshop on "Creating and Testing Mathematical Models to Understand Stem Cell Fate Decisions."
- May 15, 2016: Undergraduate lab members Ms. Natalie Azevedo and Ms. Stephanie Ruiz graduate!! Natalie received an award for being an "Outstanding Applied Mathematics Student" and Stephanie is one of two students to graduate from the joint UC Merced-UC Berkeley credential program through CalTeach.
- May 6, 2016: Graduate students Mario Banuelos, Rubi Almanza and Lasith Adhikari, along with Prof Roummel Marcia and Prof Suzanne Sindi get paper accepted at the 2016 IEEE Engineering in Medicine and Biology Society (EMBS)!
- April 27, 2016: Graduate Students Mario Banuelos, Rubi Almanza and Lasith Adhikari, along with Prof Roummel Marcia and Prof Suzanne Sindi have a paper accepted at the 2016 IEEE Statistical Signal Processing Workshop (SSP)!
- February 2016: Graduate Student Mario Banuelos has first paper accepted in ICASSP Conference.
- July 2015: Jason Davis has paper accepted in Physical Review E.
- April 28, 2015: Graduate Student Jason Davis Featured on UC Merced.
- Sept 26, 2014: Structural variation methods paper accepted in Bioinformatics.
- Sept 26, 2014: Coverage of the Graduate Internship Program between UC Merced and the Joint Genome Institute.
- Sept 16, 2014: Jason Davis has first paper accepted to Applied Mathematics Letters.

### Funding:

The Sindi Lab is supported by grants from NSF through the Inspire Program (#1344279) and the NIH (R01GM100740).

### Recent Publications:

- Mathematical Modeling of
*in vivo*Prion Disease. Suzanne S. Sindi, Chapter in Prion, ISBN 978-953-51-5046-6. (2016) - Langlois, Christine R., Fen Pei, Suzanne S. Sindi, and Tricia R. Serio. "Distinct Prion Domain Sequences Ensure Efficient Amyloid Propagation by Promoting Chaperone Binding or Processing
*In Vivo*." PLoS Genet 12, no. 11 (2016): e1006417. - Vinson, David W., Jason K. Davis, Suzanne S. Sindi, and Rick Dale. "Efficient n-gram analysis in R with cmscu." Behavior Research Methods (2016): 1-13.
- Mario Banuelos, Rubi Almanza, Lasith Adhikari, Suzanne Sindi, Roummel Marcia "Constrained Variant Detection with SPaRC: Sparsity, Parental Relatedness, and Coverage." IEEE EMBS 2016.
- Banuelos, Mario, Rubi Almanza, Lasith Adhikari, Suzanne Sindi, and Roummel F. Marcia. "Sparse Genomic Structural Variant Detection: Exploiting Parent-Child Relatedness for Signal Recovery" SSP 2016.
- Banks, Tom, Flores, Kevin and Suzanne Sindi. "On analytical and numerical approaches to division and label structured population models." Applied Mathematics Letters (2016).
- Banuelos, Mario, Rubi Almanza, Lasith Adhikari, Suzanne Sindi, and Roummel F. Marcia. "Sparse Signal Recovery Methods for Variant Detection in Next-Generation Sequencing Data" ICASSP 2016
- Davis, Jason K., and Suzanne S. Sindi. "Initial condition of stochastic self-assembly." Physical Review E 93.2 (2016): 022109.
- Sindi, Suzanne S., and Rick Dale. "Culturomics as a Data Playground for Tests of Selection: Mathematical Approaches to Detecting Selection in Word Use." Journal of Theoretical Biology (2016).
- Davis, Jason K., and Suzanne S. Sindi. "A mathematical model of the dynamics of prion aggregates with chaperone-mediated fragmentation." Journal of mathematical biology (2015): 1-24.
- Characterization of Structural Variants with Single Molecule and Hybrid Sequencing Approaches; Anna Ritz, Ali Bashir, Suzanne S. Sindi, David Hsu, Iman Hajirasouliha, Benjamin J. Raphael. Bioinformatics (2014).
- A Study in Nucleated Polymerization Models of Protein Aggregation; Jason K Davis and Suzanne S. Sindi. Applied Mathematics Letters. (2014).
- Amyloid-associated activity contributes to the severity and toxicity of a prion phenotype; John Pezza, Janice Villali, Suzanne S. Sindi, Tricia R. Serio. Nature Communications (2014).
- A Crump-Mode-Jagers branching process model of prion loss in yeast. Peter Olofsson and Suzanne Sindi. Journal of Applied Probability (2014).
- Identification of Structural Variation. Suzanne S. Sindi and Benjamin J. Raphael. Chapter in Genome Analysis: Current Procedures and Applications (2013).

### Collaborators:

Prof Sindi collaborates with several faculty at UC Merced including:- Dr. Rick Dale, Cognitive Science and Dr. David Ardell, QSB: Emergence and evolution of linguistic phenomena
- Dr. Aaron Hernday and Dr. Clarissa Nobile, Biology: Dynamics and Genomics of Yeast
- Dr. Roummel Marcia, Applied Mathematics: Mathematical optimization and computational genomics.

- Dr. H.T. Banks and Dr. Kevin Flores, North Carolina State University: inverse problems in prion biology
- Dr. Karin Leiderman, Colorado School of Mines: Protein diffusion and blood coagulation dynamics
- Dr. Peter Olofsson, Trinity University: Branching processes of prion aggregates
- Dr. Benjamin J. Raphael, Brown University: Structural variation identification
- Dr. Tricia R. Serio, University of Arizona: Yeast prion biology

### Current Lab Members:

- Graduate Students
- Mario Banuelos: Applied Mathematics
- Jason Davis: Applied Mathematics
- Alex Quijano: Applied Mathematics
- Eric Roberts: Applied Mathematics (Co-Advising with Prof Kevin Mitchell, Physics)
- Thaddeus Seher: Quantitative and Systems Biology (Co Advising with Prof Clarissa Nobile, Molecular and Cellular Biology)
- Michael Stobb: Applied Mathematics (Co Advising with Prof Karin Leiderman, Colorado School of Mines)

- Undergraduate Students
- Benjamin Juarez: Human Biology

### Former Lab Members:

- Dr. Marc Griesemer, Visiting Assistant Professor of Applied Mathematics: Lawrence Livermore National Laboratory
- Elizabeth Owens, Completed Master's in Applied Mathematics: Faculty at Las Positas Community College
- Stephanie Ruiz, Applied Mathematics Undergraduate: Completing CalTeach program
- Brian Sarracino-Aguilera, Engineering and Applied Mathematics: Master's Program Long Beach State
- Megan Schill, Chemistry Undergraduate: PhD program in Chemistry at CalTech.
- Marisela Torres, Applied Mathematics Undergraduate: Master's Program Fresno State
- Natalie Azevedo, Applied Mathematics; Outstanding Graduating Mathematics Student (2016)