Handbook of Computational Molecular Biology: Edited by Srinivas Aluru. - Suzanne S. Sindi (Briefings Bioinform., 2007)

A geometric approach for classification and comparison of structural variants. - Suzanne S. Sindi; Elena Helman; Ali Bashir; Benjamin J. Raphael (Bioinform., 2009)

Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. - Suzanne S. Sindi; Benjamin J. Raphael (J. Comput. Biol., 2010)

Workshop: Characterization of structural variants with next generation DNA sequencing. - Benjamin J. Raphael; Suzanne S. Sindi; Anna M. Ritz; Ali Bashir (ICCABS, 2011)

Identification of polymorphic inversions from genotypes. - Alejandro Cáceres; Suzanne S. Sindi; Benjamin J. Raphael; Mario Cáceres; Juan R. González (BMC Bioinform., 2012)

Characterization of structural variants with single molecule and hybrid sequencing approaches. - Anna M. Ritz; Ali Bashir; Suzanne S. Sindi; David Hsu; Iman Hajirasouliha; Benjamin J. Raphael (Bioinform., 2014)

A Crump-Mode-Jagers Branching Process Model of Prion Loss in Yeast. - Peter Olofsson; Suzanne S. Sindi (J. Appl. Probab., 2014)

A study in nucleated polymerization models of protein aggregation. - Jason K. Davis; Suzanne S. Sindi (Appl. Math. Lett., 2015)

Constrained variant detection with SPaRC: Sparsity, parental relatedness, and coverage. - Mario Banuelos; Rubi Almanza; Lasith Adhikari; Roummel F. Marcia; Suzanne Sindi (EMBC, 2016)

Sparse signal recovery methods for variant detection in next-generation sequencing data. - Mario Banuelos; Rubi Almanza; Lasith Adhikari; Suzanne Sindi; Roummel F. Marcia (ICASSP, 2016)

Sparse genomic structural variant detection: Exploiting parent-child relatedness for signal recovery. - Mario Banuelos; Rubi Almanza; Lasith Adhikari; Roummel F. Marcia; Suzanne Sindi (SSP, 2016)

On analytical and numerical approaches to division and label structured population models. - H. T. Banks; Kevin B. Flores; Suzanne S. Sindi (Appl. Math. Lett., 2016)

Sparse diploid spatial biosignal recovery for genomic variation detection. - Mario Banuelos; Lasith Adhikari; Rubi Almanza; Andrew Fujikawa; Jonathan Sahagun; Katharine Sanderson; Melissa Spence; Suzanne Sindi; Roummel F. Marcia (MeMeA, 2017)

Nonconvex regularization for sparse genomic variant signal detection. - Mario Banuelos; Lasith Adhikari; Rubi Almanza; Andrew Fujikawa; Jonathan Sahagun; Katharine Sanderson; Melissa Spence; Suzanne Sindi; Roummel F. Marcia (MeMeA, 2017)

Detecting Novel Structural Variants In Genomes By Leveraging Parent-Child Relatedness. - Melissa Spence; Mario Banuelos; Roummel F. Marcia; Suzanne Sindi (BIBM, 2018)

Structural Variant Prediction in Extended Pedigrees Through Sparse Negative Binomial Genome Signal Recovery. - Mario Banuelos; Suzanne Sindi; Roummel F. Marcia (EMBC, 2018)

Negative Binomial Optimization for Biomedical Structural Variant Signal Reconstruction. - Mario Banuelos; Suzanne Sindi; Roummel F. Marcia (ICASSP, 2018)

Fine Tuning Sparsity Penalties to Improve Structural Variant Detection. - Xiaolong Chen; Hansell Perez; Melissa Spence; Roummel F. Marcia; Suzanne Sindi (BIBM, 2019)

Predicting Novel and Inherited Variants in Parent-Child Trios. - Melissa Spence; Mario Banuelos; Roummel F. Marcia; Suzanne Sindi (MeMeA, 2019)

Detecting novel genomic structural variants through negative binomial optimization. - Andrew Lazar; Mario Banuelos; Suzanne Sindi; Roummel F. Marcia (ACSSC, 2020)

A Neural Network Approach for Anomaly Detection in Genomic Signals. - Erica Sawyer; Mario Banuelos; Roummel F. Marcia; Suzanne Sindi (APSIPA, 2020)

Related Inference: A Supervised Learning Approach to Detect Signal Variation in Genome Data. - Mario Banuelos; Omar DeGuchy; Suzanne Sindi; Roummel F. Marcia (EUSIPCO, 2020)

Genomic Signal Processing for Variant Detection in Diploid Parent-Child Trios. - Melissa Spence; Mario Banuelos; Roummel F. Marcia; Suzanne Sindi (EUSIPCO, 2020)

A unifying model for the propagation of prion proteins in yeast brings insight into the [PSI+] prion. - Paul Lemarre; Laurent Pujo-Menjouet; Suzanne S. Sindi (PLoS Comput. Biol., 2020)

Novel structural variant genome detection in extended pedigrees through negative binomial optimization. - Andrew Lazar; Mario Banuelos; Suzanne Sindi; Roummel F. Marcia (ACSCC, 2021)

A field guide to cultivating computational biology. - Anne E. Carpenter; Casey S. Greene; Piero Carnici; Benilton S. Carvalho; Michiel de Hoon; Stacey D. Finley; Kim-Anh Lê Cao; Jerry S. H. Lee; Luigi Marchionni; Suzanne Sindi; Fabian J. Theis; Gregory P. Way; et al. (CoRR, 2021)

A Statistical Model of Word Rank Evolution. - Alex John Quijano; Rick Dale; Suzanne Sindi (CoRR, 2021)

ACTIVA: realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders. - Abbas-Ali Heydari; Oscar A. Davalos; Lihong Zhao; Katrina K. Hoyer; Suzanne S. Sindi (Bioinform., 2022)

N-ACT: An Interpretable Deep Learning Model for Automatic Cell Type and Salient Gene Identification. - Abbas-Ali Heydari; Oscar A. Davalos; Katrina K. Hoyer; Suzanne S. Sindi (CoRR, 2022)

Conservative finite volume method on deforming geometries: The case of protein aggregation in dividing yeast cells. - Abbas-Ali Heydari; Suzanne S. Sindi; Maxime Theillard (J. Comput. Phys., 2022)

A structured model and likelihood approach to estimate yeast prion propagon replication rates and their asymmetric transmission. - Fabian Santiago; Suzanne S. Sindi (PLoS Comput. Biol., 2022)

Genetic Variant Detection Over Generations: Sparsity-Constrained Optimization Using Block-Coordinate Descent. - Mohammed Aburidi; Mario Banuelos; Suzanne Sindi; Roummel F. Marcia (MeMeA, 2023)

Inferring gene regulatory networks using transcriptional profiles as dynamical attractors. - Ruihao Li 005; Jordan C. Rozum; Morgan M. Quail; Mohammad N. Qasim; Suzanne S. Sindi; Clarissa J. Nobile; Réka Albert; Aaron D. Hernday (PLoS Comput. Biol., 2023)

Sparse Negative Binomial Signal Recovery for Genomic Variant Prediction in Diploid Species. - Jocelyn Ornelas Munoz; Erica M. Rutter; Mario Banuelos; Suzanne S. Sindi; Roummel F. Marcia (EMBC, 2024)

A new look at TFPI inhibition of factor X activation. - Fabian Santiago; Amandeep Kaur; Shannon Bride; Dougald Monroe; Karin Leiderman; Suzanne S. Sindi (PLoS Comput. Biol., 2024)

Enhancing generalizability of model discovery across parameter space with multi-experiment equation learning (ME-EQL). - Maria-Veronica Ciocanel; John T. Nardini; Kevin B. Flores; Erica M. Rutter; Suzanne S. Sindi; Alexandria Volkening (CoRR, 2025)