Publications

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2018

Differentially Private ANOVA Testing. Z. Campbell, A. Bray, A. Ritz, A. Groce. To appear in the proceedings of ICDIS 2018.

Programming the Central Dogma: An Integrated Unit on Computer Science and Molecular Biology Concepts. A. Ritz. To appear in the proceedings of SIGCSE 2018.

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. To appear in Genes & Development.

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. Software

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.Software

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. Software Watch

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. Software

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. Software Watch

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. Software

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. Software

< 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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Contact

Biology Department
Reed College
3203 SE Woodstock Blvd.
Portland, OR 97202-8199

Email aritz-at-reed-dot-edu

CV Curriculum Vitae [pdf]

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