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Suzanne Sindi

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Papers

Ciocanel MV, Nardini JT, Flores KB, Rutter EM, Sindi SS, Volkening A. (2026). Enhancing generalizability of model discovery across parameter space with multi-experiment equation learning for biological systems. PLoS computational biology, 22(4)

Ginsberg AG, Ahnström J, Crawley JTB, Leiderman K, Monroe DM, Neeves KB, Sindi SF, Fogelson AL. (2026). Mechanisms of thrombin inhibition by protein S and the TFPIα-fVshort-protein S complex. Biophysical journal

Madrigal J, Monroe DM, Sindi SS, Leiderman K. (2025). Mathematical analysis of emicizumab: affinity-driven complex formation and lipid surface reactions. Journal of thrombosis and haemostasis : JTH

Madrigal J, Monroe DM, Sindi SS, Leiderman K. (2024). Modeling the distribution of enzymes on lipid vesicles: A novel framework for surface-mediated reactions in coagulation. Mathematical biosciences

Kent A, Leiderman K, Nelson AC, Sindi SS, Stadt MM, Xiong LI, Zhang Y. (2024). Studying the Effects of Oral Contraceptives on Coagulation Using a Mathematical Modeling Approach. Mathematical modeling for women's health : Collaborative Workshop for Women in Mathematical Biolog. Collaborative Workshop for Women in Mathematical Biology (2022), (155)

Stobb MT, Neeves KB, Monroe DM, Sindi SS, Leiderman K, Fogelson AL. (2024). Mathematical modeling identifies clotting factor combinations that modify thrombin generation in normal and factor VIII-, IX-, or XI-deficient blood. Research and practice in thrombosis and haemostasis, 8(7)

Santiago F, Kaur A, Bride S, Monroe D, Leiderman K, Sindi S. (2024). A new look at TFPI inhibition of factor X activation. PLoS computational biology, 20(11)

Tejeda-Garibay S, Zhao L, Hum NR, Pimentel M, Diep AL, Amiri B, Sindi SS, Weilhammer DR, Loots GG, Hoyer KK. (2023). Host tracheal and intestinal microbiomes inhibit Coccidioides growth in vitro. bioRxiv : the preprint server for biology

Santiago F, Sindi S. (2022). A structured model and likelihood approach to estimate yeast prion propagon replication rates and their asymmetric transmission. PLoS computational biology, 18(7)

Agusto FB, Erovenko IV, Fulk A, Abu-Saymeh Q, Romero-Alvarez D, Ponce J, Sindi S, Ortega O, Saint Onge JM, Peterson AT. (2022). To isolate or not to isolate: the impact of changing behavior on COVID-19 transmission. BMC public health, 22(1)

Heydari AA, Davalos OA, Zhao L, Hoyer KK, Sindi SS. (2022). ACTIVA: realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders. Bioinformatics (Oxford, England)

Agusto FB, Erovenko IV, Fulk A, Abu-Saymeh Q, Romero-Alvarez D, Ponce J, Sindi S, Ortega O, Saint Onge JM, Peterson AT. (2022). Correction: To isolate or not to isolate: the impact of changing behavior on COVID-19 transmission. BMC public health, 22(1)

Guzman-Cole C, Santiago F, Garsevanyan S, Sindi S, Barlow M. (2021). Distribution of β-Lactamase Genes in Clinical Isolates from California Central Valley Hospital Deviates from the United States Nationwide Trends. Antibiotics (Basel, Switzerland), 10(5)

Way GP, Greene CS, Carninci P, Carvalho BS, de Hoon M, Finley S, Gosline SJC, Lȇ Cao KA, Lee JSH, Marchionni L, Robine N, Sindi SS, Theis FJ, Yang JYH, Carpenter AE, Fertig EJ. (2021). A field guide to cultivating computational biology. PLoS biology, 19(10)

Santiago F, Doscher E, Kim J, Camps M, Meza J, Sindi S, Barlow M. (2020). Growth rate assays reveal fitness consequences of β-lactamases. PloS one, 15(1)

Lemarre P, Pujo-Menjouet L, Sindi SS. (2020). A unifying model for the propagation of prion proteins in yeast brings insight into the [PSI+] prion. PLoS computational biology, 16(5)

Villali J, Dark J, Brechtel TM, Pei F, Sindi SS, Serio TR. (2020). Nucleation seed size determines amyloid clearance and establishes a barrier to prion appearance in yeast. Nature structural & molecular biology, 27(6)

Banwarth-Kuhn M, Sindi S. (2020). How and why to build a mathematical model: A case study using prion aggregation. The Journal of biological chemistry, 295(15)

Link KG, Stobb MT, Sorrells MG, Bortot M, Ruegg K, Manco-Johnson MJ, Di Paola JA, Sindi SS, Fogelson AL, Leiderman K, Neeves KB. (2020). A mathematical model of coagulation under flow identifies factor V as a modifier of thrombin generation in hemophilia A. Journal of thrombosis and haemostasis : JTH, 18(2)

Stobb MT, Monroe DM, Leiderman K, Sindi SS. (2019). Assessing the impact of product inhibition in a chromogenic assay. Analytical biochemistry, (580)

Link KG, Stobb MT, Di Paola J, Neeves KB, Fogelson AL, Sindi SS, Leiderman K. (2018). A local and global sensitivity analysis of a mathematical model of coagulation and platelet deposition under flow. PloS one, 13(7)

Lemarre P, Pujo-Menjouet L, Sindi SS. (2018). Generalizing a mathematical model of prion aggregation allows strain coexistence and co-stability by including a novel misfolded species. Journal of mathematical biology, 78(1-2)

Valentine KM, Davini D, Lawrence TJ, Mullins GN, Manansala M, Al-Kuhlani M, Pinney JM, Davis JK, Beaudin AE, Sindi SS, Gravano DM, Hoyer KK. (2018). CD8 Follicular T Cells Promote B Cell Antibody Class Switch in Autoimmune Disease. Journal of immunology (Baltimore, Md. : 1950), 201(1)

Pei F, DiSalvo S, Sindi SS, Serio TR. (2017). A dominant-negative mutant inhibits multiple prion variants through a common mechanism. PLoS genetics, 13(10)

Langlois CR, Pei F, Sindi SS, Serio TR. (2016). Distinct Prion Domain Sequences Ensure Efficient Amyloid Propagation by Promoting Chaperone Binding or Processing In Vivo. PLoS genetics, 12(11)

Sindi SS, Dale R. (2016). Culturomics as a data playground for tests of selection: Mathematical approaches to detecting selection in word use. Journal of theoretical biology, (405)

Vinson DW, Davis JK, Sindi SS, Dale R. (2016). Efficient n-gram analysis in R with cmscu. Behavior research methods, 48(3)

Davis JK, Sindi SS. (2015). A Study in Nucleated Polymerization Models of Protein Aggregation. Applied mathematics letters, (40)

Davis JK, Sindi SS. (2016). A mathematical model of the dynamics of prion aggregates with chaperone-mediated fragmentation. Journal of mathematical biology, 72(6)

Pezza JA, Villali J, Sindi SS, Serio TR. (2014). Amyloid-associated activity contributes to the severity and toxicity of a prion phenotype. Nature communications, (5)

Sindi SS, Olofsson P. (2013). A Discrete-Time Branching Process Model of Yeast Prion Curing Curves. Mathematical population studies, 20(1)

Sindi SS, Onal S, Peng LC, Wu HT, Raphael BJ. An integrative probabilistic model for identification of structural variation in sequencing data. Genome biology, 13(3)

Cáceres A, Sindi SS, Raphael BJ, Cáceres M, González JR. (2012). Identification of polymorphic inversions from genotypes. BMC bioinformatics, (13)

Derdowski A, Sindi SS, Klaips CL, DiSalvo S, Serio TR. (2010). A size threshold limits prion transmission and establishes phenotypic diversity. Science (New York, N.Y.), 330(6004)

Sindi SS, Serio TR. (2009). Prion dynamics and the quest for the genetic determinant in protein-only inheritance. Current opinion in microbiology, 12(6)

Sindi SS, Hunt BR, Yorke JA. (2008). Duplication count distributions in DNA sequences. Physical review. E, Statistical, nonlinear, and soft matter physics, 78(6 Pt 1)

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