PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data

by Chen, Ken, McLellan, Michael D., Ding, Li, Wendl, Michael C., Kasai, Yumi, Wilson, Richard K., Mardis, Elaine R.
Published 2007

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

by Niu, Beifang, Ye, Kai, Zhang, Qunyuan, Lu, Charles, Xie, Mingchao, McLellan, Michael D., Wendl, Michael C., Ding, Li
Published 2014

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

by Koboldt, Daniel C., Chen, Ken, Wylie, Todd, Larson, David E., McLellan, Michael D., Mardis, Elaine R., Weinstock, George M., Wilson, Richard K., Ding, Li
Published 2009

Reduced PU.1 expression causes myeloid progenitor expansion and increased leukemia penetrance in mice expressing PML-RARα

by Walter, Matthew J., Park, John S., Ries, Rhonda E., Lau, Steven K. M., McLellan, Michael, Jaeger, Sara, Wilson, Richard K., Mardis, Elaine R., Ley, Timothy J.
Published 2005

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

by Koboldt, Daniel C., Zhang, Qunyuan, Larson, David E., Shen, Dong, McLellan, Michael D., Lin, Ling, Miller, Christopher A., Mardis, Elaine R., Ding, Li, Wilson, Richard K.
Published 2012

Clonal Evolution Revealed by Whole Genome Sequencing in a Case of Primary Myelofibrosis Transformed to Secondary Acute Myeloid Leukemia

by Engle, Elizabeth K., Fisher, Daniel A.C., Miller, Christopher A., McLellan, Michael D., Fulton, Robert S., Moore, Deborah M., Wilson, Richard K., Ley, Timothy J., Oh, Stephen T.
Published in Leukemia (2014)

BreakPoint Surveyor: a pipeline for structural variant visualization

by Wyczalkowski, Matthew A, Wylie, Kristine M, Cao, Song, McLellan, Michael D, Flynn, Jennifer, Huang, Mo, Ye, Kai, Fan, Xian, Chen, Ken, Wendl, Michael C, Ding, Li
Published in Bioinformatics (2017)

HPV-EM: an accurate HPV detection and genotyping EM algorithm

by Inkman, Matthew J., Jayachandran, Kay, Ellis, Thomas M., Ruiz, Fiona, McLellan, Michael D., Miller, Christopher A., Wu, Yufeng, Ojesina, Akinyemi I., Schwarz, Julie K., Zhang, Jin
Published in Sci Rep (2020)

Mutation of a common amino acid in NKX2.5 results in dilated cardiomyopathy in two large families

by Hanley, Alan, Walsh, Katie A., Joyce, Caroline, McLellan, Michael A., Clauss, Sebastian, Hagen, Amaya, Shea, Marisa A., Tucker, Nathan R., Lin, Honghuang, Fahy, Gerard J., Ellinor, Patrick T.
Published in BMC Med Genet (2016)

CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data

by Zhang, Qunyuan, Ding, Li, Larson, David E., Koboldt, Daniel C., McLellan, Michael D., Chen, Ken, Shi, Xiaoqi, Kraja, Aldi, Mardis, Elaine R., Wilson, Richard K., Borecki, Ingrid B., Province, Michael A.
Published 2010

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

by Ellrott, Kyle, Bailey, Matthew H., Saksena, Gordon, Covington, Kyle R., Kandoth, Cyriac, Stewart, Chip, Hess, Julian, Ma, Singer, McLellan, Michael, Sofia, Heidi J., Hutter, Carolyn, Getz, Gad, Wheeler, David, Ding, Li
Published in Cell Syst (2018)

Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif

by Hamilton, Mark P., Rajapakshe, Kimal, Hartig, Sean M., Reva, Boris, McLellan, Michael D., Kandoth, Cyriac, Ding, Li, Zack, Travis I., Gunaratne, Preethi H., Wheeler, David A., Coarfa, Cristian, McGuire, Sean E.
Published 2013

Clinical outcomes and differential effects of PI3K pathway mutation in obese versus non-obese patients with cervical cancer

by Grigsby, Perry, Elhammali, Adnan, Ruiz, Fiona, Markovina, Stephanie, McLellan, Michael D., Miller, Christopher A., Chundury, Anupama, Ta, Ngoc-Anh L., Rashmi, Ramachandran, Pfeifer, John D., Fulton, Robert S., DeWees, Todd, Schwarz, Julie K.
Published in Oncotarget (2017)

Caspase-9 is required for normal hematopoietic development and protection from alkylator-induced DNA damage in mice

by Lu, Elise Peterson, McLellan, Michael, Ding, Li, Fulton, Robert, Mardis, Elaine R., Wilson, Richard K., Miller, Christopher A., Westervelt, Peter, DiPersio, John F., Link, Daniel C., Walter, Matthew J., Ley, Timothy J., Graubert, Timothy A.
Published in Blood (2014)

Pan-cancer analysis of somatic mutations across 21 neuroendocrine tumor types

by Cao, Yanan, Zhou, Weiwei, Li, Lin, Wang, Jiaqian, Gao, Zhibo, Jiang, Yiran, Jiang, Xiuli, Shan, Aijing, Bailey, Matthew H., Huang, Kuan-lin, Sun, Sam Q., McLellan, Michael D., Niu, Beifang, Wang, Weiqing, Ding, Li, Ning, Guang
Published in Cell Res (2018)

Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma

by Gutmann, David H., McLellan, Michael D., Hussain, Ibrahim, Wallis, John W., Fulton, Lucinda L., Fulton, Robert S., Magrini, Vincent, Demeter, Ryan, Wylie, Todd, Kandoth, Cyriac, Leonard, Jeffrey R., Guha, Abhijit, Miller, Christopher A., Ding, Li, Mardis, Elaine R.
Published 2013

Novel MEK1 Mutation Identified by Mutational Analysis of Epidermal Growth Factor Receptor Signaling Pathway Genes in Lung Adenocarcinoma

by Marks, Jenifer L., Gong, Yixuan, Chitale, Dhananjay, Golas, Ben, McLellan, Michael D., Kasai, Yumi, Ding, Li, Mardis, Elaine R., Wilson, Richard K., Solit, David, Levine, Ross, Michel, Kathrin, Thomas, Roman K., Rusch, Valerie W., Ladanyi, Marc, Pao, William
Published 2008

BreakTrans: uncovering the genomic architecture of gene fusions

by Chen, Ken, Navin, Nicholas E, Wang, Yong, Schmidt, Heather K, Wallis, John W, Niu, Beifang, Fan, Xian, Zhao, Hao, McLellan, Michael D, Hoadley, Katherine A, Mardis, Elaine R, Ley, Timothy J, Perou, Charles M, Wilson, Richard K, Ding, Li
Published 2013

BreakDancer: An algorithm for high resolution mapping of genomic structural variation

by Chen, Ken, Wallis, John W., McLellan, Michael D., Larson, David E., Kalicki, Joelle M., Pohl, Craig S., McGrath, Sean D., Wendl, Michael C., Zhang, Qunyuan, Locke, Devin P., Shi, Xiaoqi, Fulton, Robert S., Ley, Timothy J., Wilson, Richard K., Ding, Li, Mardis, Elaine R.
Published 2009

Recurrent DNMT3A Mutations in Patients with Myelodysplastic Syndromes

by Walter, Matthew J., Ding, Li, Shen, Dong, Shao, Jin, Grillot, Marcus, McLellan, Michael, Fulton, Robert, Schmidt, Heather, Kalicki-Veizer, Joelle, O’Laughlin, Michelle, Kandoth, Cyriac, Baty, Jack, Westervelt, Peter, DiPersio, John F., Mardis, Elaine R, Wilson, Richard K., Ley, Timothy J., Graubert, Timothy A.
Published 2011