FiNGS: high quality somatic mutations using filters for next generation sequencing

by Wardell, Christopher Paul, Ashby, Cody, Bauer, Michael Anton
Published in BMC Bioinformatics (2021)

New enumeration algorithm for protein structure comparison and classification

by Ashby, Cody, Johnson, Daniel, Walker, Karl, Kanj, Iyad A, Xia, Ge, Huang, Xiuzhen
Published 2013

eMBI: Boosting Gene Expression-based Clustering for Cancer Subtypes

by Chang, Zheng, Wang, Zhenjia, Ashby, Cody, Zhou, Chuan, Li, Guojun, Zhang, Shuzhong, Huang, Xiuzhen
Published 2014

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data

by Chang, Zheng, Li, Guojun, Liu, Juntao, Zhang, Yu, Ashby, Cody, Liu, Deli, Cramer, Carole L, Huang, Xiuzhen
Published in Genome Biol (2015)

SPARCoC: A New Framework for Molecular Pattern Discovery and Cancer Gene Identification

by Ma, Shiqian, Johnson, Daniel, Ashby, Cody, Xiong, Donghai, Cramer, Carole L., Moore, Jason H., Zhang, Shuzhong, Huang, Xiuzhen
Published in PLoS One (2015)

DNAp: A Pipeline for DNA-seq Data Analysis

by Causey, Jason L., Ashby, Cody, Walker, Karl, Wang, Zhiping Paul, Yang, Mary, Guan, Yuanfang, Moore, Jason H., Huang, Xiuzhen
Published in Sci Rep (2018)

Enhancing cancer clonality analysis with integrative genomics

by Peterson, Erich A, Bauer, Michael A, Chavan, Shweta S, Ashby, Cody, Weinhold, Niels, Heuck, Christoph J, Morgan, Gareth J, Johann, Donald J
Published in BMC Bioinformatics (2015)

TarPan: an easily adaptable targeted sequencing panel viewer for research and clinical use

by Ashby, Cody, Rutherford, Michael, Bauer, Michael A., Peterson, Erich A., Wang, Yan, Boyle, Eileen M., Wardell, Christopher P., Walker, Brian A.
Published in BMC Bioinformatics (2020)

Differential RNA splicing as a potentially important driver mechanism in multiple myeloma

by Bauer, Michael A., Ashby, Cody, Wardell, Christopher, Boyle, Eileen M., Ortiz, Maria, Flynt, Erin, Thakurta, Anjan, Morgan, Gareth, Walker, Brian A.
Published in Haematologica (2020)

3195 Genomic Analysis of Primary Plasma Cell Leukemia reveals Complex Cytogenetic Alterations and High Risk Mutational Patterns

by Schinke, Carolina, Boyle, Eileen, Ashby, Cody, Wang, Yan, Christopher Wardell, Davies, Thanendrarajan, Sharmilan, Zangari, maurizio, van Rhee, Frits, Morgan, Gareth, Walker, Brian
Published in J Clin Transl Sci (2019)

Loss of heterozygosity as a marker of homologous repair deficiency in multiple myeloma: a role for PARP inhibition?

by Pawlyn, Charlotte, Loehr, Andrea, Ashby, Cody, Tytarenko, Ruslana, Deshpande, Shayu, Sun, James, Fedorchak, Kyle, Mughal, Tariq, Davies, Faith E., Walker, Brian A., Morgan, Gareth J.
Published in Leukemia (2018)

The functional epigenetic landscape of aberrant gene expression in molecular subgroups of newly diagnosed multiple myeloma

by Choudhury, Samrat Roy, Ashby, Cody, Tytarenko, Ruslana, Bauer, Michael, Wang, Yan, Deshpande, Shayu, Den, Judith, Schinke, Carolina, Zangari, Maurizio, Thanendrarajan, Sharmilan, Davies, Faith E., van Rhee, Frits, Morgan, Gareth J., Walker, Brian A.
Published in J Hematol Oncol (2020)

Poor overall survival in hyperhaploid multiple myeloma is defined by double-hit bi-allelic inactivation of TP53

by Ashby, Cody, Tytarenko, Ruslana G., Wang, Yan, Weinhold, Niels, Johnson, Sarah K., Bauer, Michael, Wardell, Christopher P., Schinke, Carolina, Thanendrarajan, Sharmilan, Zangari, Mauricio, van Rhee, Frits, Davies, Faith E., Sawyer, Jeffrey R., Morgan, Gareth J., Walker, Brian A.
Published in Oncotarget (2019)

The level of deletion 17p and bi-allelic inactivation of TP53 has a significant impact on clinical outcome in multiple myeloma

by Thanendrarajan, Sharmilan, Tian, Erming, Qu, Pingping, Mathur, Pankaj, Schinke, Carolina, van Rhee, Frits, Zangari, Maurizio, Rasche, Leo, Weinhold, Niels, Alapat, Daisy, Bellamy, William, Ashby, Cody, Mattox, Sandra, Epstein, Joshua, Yaccoby, Shmuel, Barlogie, Bart, Hoering, Antje, Bauer, Michael, Walker, Brian A., Davies, Faith E., Morgan, Gareth J.
Published in Haematologica (2017)

Genomic analysis of primary plasma cell leukemia reveals complex structural alterations and high-risk mutational patterns

by Schinke, Carolina, Boyle, Eileen M., Ashby, Cody, Wang, Yan, Lyzogubov, Valeriy, Wardell, Christopher, Qu, Pingping, Hoering, Antje, Deshpande, Shayu, Ryan, Katie, Thanendrarajan, Sharmilan, Mohan, Meera, Yarlagadda, Naveen, Khan, Maliha, Choudhury, Samrat Roy, Zangari, Maurizio, van Rhee, Frits, Davies, Faith, Barlogie, Bart, Morgan, Gareth, Walker, Brian A.
Published in Blood Cancer J (2020)

Microhomology-mediated end joining drives complex rearrangements and overexpression of MYC and PVT1 in multiple myeloma

by Mikulasova, Aneta, Ashby, Cody, Tytarenko, Ruslana G., Qu, Pingping, Rosenthal, Adam, Dent, Judith A., Ryan, Katie R., Bauer, Michael A., Wardell, Christopher P., Hoering, Antje, Mavrommatis, Konstantinos, Trotter, Matthew, Deshpande, Shayu, Yaccoby, Shmuel, Tian, Erming, Keats, Jonathan, Auclair, Daniel, Jackson, Graham H., Davies, Faith E., Thakurta, Anjan, Morgan, Gareth J., Walker, Brian A.
Published in Haematologica (2020)

Clonal evolution in myeloma: the impact of maintenance lenalidomide and depth of response on the genetics and sub-clonal structure of relapsed disease in uniformly treated newly di...

by Jones, John R., Weinhold, Niels, Ashby, Cody, Walker, Brian A., Wardell, Chris, Pawlyn, Charlotte, Rasche, Leo, Melchor, Lorenzo, Cairns, David A., Gregory, Walter M., Johnson, David, Begum, Dil B., Ellis, Sidra, Sherborne, Amy L., Cook, Gordon, Kaiser, Martin F., Drayson, Mark T., Owen, Roger G., Jackson, Graham H., Davies, Faith E., Greaves, Mel, Morgan, Gareth J.
Published in Haematologica (2019)

The molecular make up of smoldering myeloma highlights the evolutionary pathways leading to multiple myeloma

by Boyle, Eileen M., Deshpande, Shayu, Tytarenko, Ruslana, Ashby, Cody, Wang, Yan, Bauer, Michael A., Johnson, Sarah K., Wardell, Christopher P., Thanendrarajan, Sharmilan, Zangari, Maurizio, Facon, Thierry, Dumontet, Charles, Barlogie, Bart, Arbini, Arnaldo, Rustad, Even H., Maura, Francesco, Landgren, Ola, Zhan, Fenghuang, van Rhee, Frits, Schinke, Carolina, Davies, Faith E., Morgan, Gareth J., Walker, Brian A.
Published in Nat Commun (2021)

Clonal selection and double-hit events involving tumor suppressor genes underlie relapse in myeloma

by Weinhold, Niels, Ashby, Cody, Rasche, Leo, Chavan, Shweta S., Stein, Caleb, Stephens, Owen W., Tytarenko, Ruslana, Bauer, Michael A., Meissner, Tobias, Deshpande, Shayu, Patel, Purvi H., Buzder, Timea, Molnar, Gabor, Peterson, Erich A., van Rhee, Frits, Zangari, Maurizio, Thanendrarajan, Sharmilan, Schinke, Carolina, Tian, Erming, Epstein, Joshua, Barlogie, Bart, Davies, Faith E., Heuck, Christoph J., Walker, Brian A, Morgan, Gareth J.
Published in Blood (2016)

Revealing the Impact of Structural Variants in Multiple Myeloma

by Rustad, Even H., Yellapantula, Venkata D., Glodzik, Dominik, Maclachlan, Kylee H., Diamond, Benjamin, Boyle, Eileen M., Ashby, Cody, Blaney, Patrick, Gundem, Gunes, Hultcrantz, Malin, Leongamornlert, Daniel, Angelopoulos, Nicos, Agnelli, Luca, Auclair, Daniel, Zhang, Yanming, Dogan, Ahmet, Bolli, Niccolò, Papaemmanuil, Elli, Anderson, Kenneth C., Moreau, Philippe, Avet-Loiseau, Hervé, Munshi, Nikhil C., Keats, Jonathan J., Campbell, Peter J., Morgan, Gareth J., Landgren, Ola, Maura, Francesco
Published in Blood Cancer Discov (2020)