Publications
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2022
Temperature mediated transgenerational plasticity influences movement behaviour in the green algae Chlamydomonas reinhardtii. H. Meier, I. Schuman, T. Layden, A. Ritz, C. Kremer, and S. Fey. Functional Ecology. In press.
FiT: Fiber-Based Tensor Completion for Drug Repurposing. A. Bumin, A. Ritz, D. Slonim, T. Kaveci, and K. Huang. 13th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) 2022. Best Student Paper Award.
Transformer Neural Networks for Protein Family and Interaction Prediction Tasks. A. Nambiar, M. Heflin, S. Liu, J. M. Forsyth, S. Maslov, M. Hopkins, and A. Ritz. Journal of Computational Biology 2022.
Reconciling Signaling Pathway Databases with Network Topologies. T. Rubel, P. Singh, and A. Ritz. Proceedings of the Pacific Symposium on Biocomputing 2022.
2021
Ten Simple Rules for Attending Your First Conference. E. Leininger, K. Shaw, N. Moshiri, K. Neiles, G. Onsongo, and A. Ritz. PLOS Computational Biology 2021. [website]
Graphery: interactive tutorials for biological network algorithms. H. Zeng, J. Zhang, G. A. Preising, T. Rubel, P. Singh, and A. Ritz. Nucleic Acids Research 2021. [website]
Development of combination therapies to induce durable responses in kidney cancers. H. Lue, D. Derrick, S. Rao, A. Van Gaest, L. Cheng, J. Podolak, S. Lawson, C. Xue, D. Garg, R. White III, C. Ryan, J. Drake, A. Ritz, L. M. Heiser, and G. V. Thomas. Cell Reports Medicine 2021.
2020
The Drosophila melanogaster Rab GAP RN-tre Regulates Non-muscle Myosin II Localization and Function through the Rho Pathway. A. Platenkamp, E. Detmar, L. Sepulveda, A. Ritz, S.L. Rogers, and D. A. Applewhite. Molecular Biology of the Cell 2020.
Augmenting Signaling Pathway Reconstructions. T. Rubel and A. Ritz. 11th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) 2020.
Transforming the Language of Life: Transformer Neural Networks for Protein Prediction Tasks. A. Nambiar, M. Heflin, S. Liu, S. Maslov, M. Hopkins, and A. Ritz. 11th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) 2020.
Lowering the Barrier to Learn about Computational Research through a Course-Based Conference Experience. A. R. Lazarte and A. Ritz. 5th International Conference on Research in Equity and Sustained Participation in Engineering, Computing, and Technology (RESPECT) 2020.
MsPAC: A Tool for Haplotype-phased Structural Variant Detection. O. L. Rodriguez, A. Ritz, A. J. Sharp, A. Bashir. Bioinformatics.
2019
Factors Affecting Network-Based Gene Prediction Across Diverse Diseases. A. King, I. Youssef, A. Ritz. 10th Workshop on Integrative Data Analysis in Systems Biology (IDASB) 2019.
Distance Measures for Tumor Evolutionary Trees. Z. DiNardo, K. Tomlinson, A. Ritz, L. Oesper. Bioinformatics.
Hypergraph-based Connectivity Measures for Signaling Pathway Topologies. N. Franzese, A. Groce, T. M. Murali, A. Ritz. PLOS Computational Biology.
Integrating Protein Localization with Automated Signaling Pathway Reconstruction. I. Youssef, J. Law, A. Ritz. BMC Bioinformatics 2019. [BIBM 2018 version]
Improved Differentially Private Analysis of Variance. M. Swanberg, I. Globus-Harris, I. Griffith, A. Ritz, A. Bray, A. Groce. 19th Privacy Enhancing Technologies Symposium (PETS) 2019. [arXiv]
Network-Based Prediction of Polygenic Disease Genes Involved in Cell Motility. M. Bern, A. King, D. A. Applewhite, A. Ritz. BMC Bioinformatics.
2018
Establishment of a cell-based assay to investigate non-muscle myosin II contractility via the Folded-gastrulation signaling pathway in Drosophila S2R+ cells. K. A. Peters, E. Detmar, L. Seulveda, C. Del Valle, R. Valsquier, A. Ritz, S. L. Rogers, D. A. Applewhite. Journal of Visualized Experiments (JoVE) (138), e58325.
Differentially Private ANOVA Testing. Z. Campbell, A. Bray, A. Ritz, A. Groce. To appear at the International Conference on Data Intelligence and Security (ICDIS 2018). [arXiv]
Programming the Central Dogma: An Integrated Unit on Computer Science and Molecular Biology Concepts. A. Ritz. ACM Special Interest Group in Computer Science Education (SIGCSE 2018). [resources]
2017
Metabolic Reprogramming Ensures Cancer Cell Survival Despite Oncogenic Signaling Blockade. H. Lue, J. Podolak, K. Kolahi, L. cheng, S. Rao, D. Garg, C. Xue, J. Rantala, J. Tyner, K. Thornburg, A. Martinez-Acevedo, J. Liu, C. Amling, C. Truillet, M. Evans, V. O'Donnell, D. Nomura, J. Drake, A. Ritz, G. Thomas. Genes & Development 2017. Oct 15;31(20):2067- 2084.
GraphSpace: Stimulating Interdisciplinary Collaborations in Network Biology. A. Bharadwaj, D. P. Singh, A. Ritz, A. N. Tegge, C. L. Poirel, P. Kraikivski, N. Adames, K. Luther, S. D. Kale, J. Peccoud, J. J. Tyson, T. M. Murali. Bioinformatics 2017. 33(19):3134-3136.
Pathway Analysis with Signaling Hypergraphs. A. Ritz, B. Avent, T. M. Murali. IEEE Transactions on Computational Biology and Bioinformatics (TCBB) 2017. 15(5):1042-1055.
2016
Pathways on Demand: Automated Reconstruction of Human Signaling Networks. A. Ritz, C. L. Poirel, A. N. Tegge, N. Sharp, A. Powell, K. Simmons, S. Kale, T. M. Murali. NPJ Systems Biology and Applications, 2:16002, 2016. Supplementary website.
2015
2014
Characterization of Structural Variants with Single Molecule and Hybrid Sequencing Approaches. A. Ritz, A. Bashir, S. Sindi, D. Hsu, I. Hajirasouliha, B.J. Raphael. Bioinformatics 2014. 30(24):3458-66.
Pathway Analysis with Signaling Hypergraphs. A. Ritz and T. M. Murali. Proceedings of the Fifth ACM Conference on Bioinformatics, Computational Biology, and Health Informatics 2014. 249–258. Nominated for Best Paper Award.
Signaling Hypergraphs. A. Ritz, A. N. Tegge, H. Kim, C. L. Poirel, T. M. Murali. Trends in Biotechnology, 32(7), 356-362, 2014. AR, ANT joint first authors.
2013
2012
Reconstructing Cancer Genome Organization. L. Oesper, A. Ritz, S. J. Aerni, R. Drebin, B. J. Raphael. BMC Bioinformatics 2012. 13(Suppl 6):S10. Special Issue of RECOMB-Seq 2012.
Algorithms for Identifying Structural Variants in Human Genomes. A. Ritz. Ph.D. Thesis, Brown University (2012)
Quantitative Phosphoproteomics Reveals SLP-76 Dependent Regulation of PAG and Src Family Kinases in T Cells. L. Cao, Y. Ding, N. Hung, K.Yu, A. Ritz, B. J. Raphael, A. R. Salomon. PLoS ONE 2014. 7,10:e46725
2011
Integrated Genomics of Ovarian Xenograft Tumor Progression and Chemotherapy Response. A. Stuckey, A. Fischer, D. H. Miller, S. Hillenmeyer, K. K. Kim, A. Ritz, R. K. Singh, B. J. Raphael, L. Brard, A. S. Brodsky. BMC Cancer 2011. 11:308.
Detection of Recurrent Rearrangement Breakpoints from Copy Number Data. A. Ritz, P. Pareis, M. M. Ittmann, C. Collins, B. J. Raphael. BMC Bioinformatics 2011. 12:114. Special Issue of RECOMB-CCB 2010.
Highly Accessed.
2010
Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements T. O'Brien, A. Ritz, B. J. Raphael, D. H. Laidlaw. IEEE Transactions on Visualization and Computer Graphics 16(6):918-26. Proceedings of the IEEE Information Visualization Conference (InfoViz) 2010.
Structural Variation Analysis with Strobe Reads. A. Ritz, A. Bashir, B. J. Raphael. Bioinformatics 2010. 26(10): 1291-1298. Special Issue of HiTSeq 2010.
ENCHILADA: Environmental Chemistry through Intelligent Atmospheric Data Analysis. D. S. Gross, R. Atlas, J. Rzeszotarski, E. Turetsky, J. Christensen, S. Benzaid, J. Olson, T. Smith, L. Steinberg, J. Sulman, A. Ritz, B. Anderson, C. Nelson, D. R. Musicant, L. Chen, D. C. Snyder, J. J. Schauer. Environmental Modelling & Software 2010. 25(6):760-769.
2009
A New Approach for Quantitative Phosphoproteomic Dissection of Signaling Pathways Applied to T Cell Receptor Activation. V. Nguyen, L. Cao, J. T. Lin, N. Hung, A. Ritz, K. Yu, R. Jianu, S. P. Ulin, B. J. Raphael, D. H. Laidlaw, L. Brossay, A. R. Salomon. Molecular and Cellular Proteomics 2009. 8: 2418-2431.
Discovery of Phosphorylation Motif Mixtures in Phosphoproteomics Data. A. Ritz, G. Shakhnarovich, A. R. Salomon, B. J. Raphael. Bioinformatics 2009. 25(1):14-21.
< 2009
A Minimum Description Length Approach to the Multiple Motif Problem. A. Ritz. Sc. M. Thesis, Brown University (2008).
Quantitative Time-Resolved Phosphoproteomic Analysis of Mast Cell Signaling. L. Cao, K. Yu, C. Banh, V. Nguyen, A. Ritz, B. J. Raphael, Y. Kawakami, T. Kawakami, A. R. Salomon, Journal of Immunology 2007. 179: 5864-5876.
Adapting K-Medians to Generate Normalized Cluster Centers. B. J. Anderson, D. S. Gross, D. R. Musicant, A. Ritz, T. G. Smith, L. E. Steinberg. Proceedings of the Sixth SIAM International Conference on Data Mining (SDM) 2006. pp165-175.
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