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
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.
- March 22, 2017: Congratulations to Sindi Lab member Mr. Mario Banuelos for receiving an Honorable Mention from the Ford Foundation Graduate Fellowship Program and Mr. Thaddeus Seher for an Honorable Mention for the Graduate Research Fellowship Program from the National Science Foundation.
- March 13, 2017: SV constrained optimization papers developed from the Archimedes REU were accepted at the Medical Measurements and Applications Conference!
- March 11, 2017: Variant detection paper accepted in ENBENG! Congratulations to Mario, Lasith, Rubi and Roummel! Great job everyone!
- March 8, 2017: The book Prion - An Overview (ISBN 978-953-51-3002-4) edited by Yusuf Tutar now available on-line! http://www.intechopen.com/books/prion-an-overview
- February 22, 2017: QSB Jonathan Anzules officially joins the Hoyer-Sindi Labs! Jonathan research will focus on the develop of systemic autoimmune disease and will be a combination of experimental, computational and modeling work! Congratulations!
- January 30, 2017: Structured population model accepted! Congratulations to everyone!
- 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.
Funding:The Sindi Lab is supported by grants from NSF through the Inspire Program (#1344279) and the NIH (R01GM100740).
- Sparse diploid spatial biosignal recovery for genomic variation detection. M.Banuelos, L. Adhikari, R. Almanza, A. Fujikawa, J. Sahagun, K. Sanderson, M. Spence, S.Sindi, and R. Marcia. Accepted to 2017 IEEE International Symposium on Medical Measurements and Applications. (In Press)
- Nonconvex regularization for sparse genomic variant signal detection. M.Banuelos, L. Adhikari, R. Almanza, A. Fujikawa, J. Sahagun, K. Sanderson, M. Spence, S.Sindi, and R. Marcia.Accepted to 2017 IEEE International Symposium on Medical Measurements and Applications. (In Press)
- Biomedical Signal Recovery: Genomic Variant Detection in Family Lineages. Mario Banuelos, Rubi Almanza, Lasith Adhikari, Suzanne Sindi, and Roummel F. Marcia. Accepted to the IEEE 5th Portuguese Meeting on Bioengineering. (In Press).
- Estimating the Rate of Prion Aggregate Amplification in Yeast with a Generation and Structured Population Model. H.T. Banks, Kevin Flores, Christine R. Langlois, Tricia R. Serio and Suzanne S. Sindi. (In Press).
- Mathematical Modeling of in vivo Prion Disease. Suzanne S. Sindi, Chapter in Prion, ISBN 978-953-51-5046-6. (2017)
- 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. Katrina Hoyer, RNA-seq Analysis in Systemic Autoimmune Disorders
- 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. Tricia R. Serio, University of Arizona: Yeast prion biology
Current Lab Members:
- Graduate Students
- Jonathan Anzules: Quantitative and Systems Biology (Co-Advising with Prof Katrina Hoyer, Molecular and Cellular Biology)
- Mario Banuelos: Applied Mathematics
- Jason Davis: Applied Mathematics
- Alex Quijano: Applied Mathematics
- Eric Roberts: Applied Mathematics (Co-Advising with Prof Kevin Mitchell, Physics)
- Fabian Santiago: Applied Mathematics (Co-Advising with Dean Juan Meza, Applied Mathematics and Prof Miriam Barlow, Molecular and Cellular Biology)
- 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)