Robust detection of alternative splicing in a population of single cells

por Welch, Joshua D., Hu, Yin, Prins, Jan F.
Publicado 2016

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data

por Welch, Joshua D., Hartemink, Alexander J., Prins, Jan F.
Publicado 2016

MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

por Welch, Joshua D., Hartemink, Alexander J., Prins, Jan F.
Publicado 2017

Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

por Welch, Joshua D, Baran-Gale, Jeanette, Perou, Charles M, Sethupathy, Praveen, Prins, Jan F
Publicado 2015

EnD-Seq and AppEnD: sequencing 3′ ends to identify nontemplated tails and degradation intermediates

por Welch, Joshua D., Slevin, Michael K., Tatomer, Deirdre C., Duronio, Robert J., Prins, Jan F., Marzluff, William F.
Publicado 2015

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data

por Singh, Darshan, Orellana, Christian F., Hu, Yin, Jones, Corbin D., Liu, Yufeng, Chiang, Derek Y., Liu, Jinze, Prins, Jan F.
Publicado 2011

BlackOPs: increasing confidence in variant detection through mappability filtering

por Cabanski, Christopher R., Wilkerson, Matthew D., Soloway, Matthew, Parker, Joel S., Liu, Jinze, Prins, Jan F., Marron, J. S., Perou, Charles M., Hayes, D. Neil
Publicado 2013

Selective single cell isolation for genomics using microraft arrays

por Welch, Joshua D., Williams, Lindsay A., DiSalvo, Matthew, Brandt, Alicia T., Marayati, Raoud, Sims, Christopher E., Allbritton, Nancy L., Prins, Jan F., Yeh, Jen Jen, Jones, Corbin D.
Publicado 2016

NeoSplice: a bioinformatics method for prediction of splice variant neoantigens

por Chai, Shengjie, Smith, Christof C, Kochar, Tavleen K, Hunsucker, Sally A, Beck, Wolfgang, Olsen, Kelly S, Vensko, Steven, Glish, Gary L, Armistead, Paul M, Prins, Jan F, Vincent, Benjamin G
Publicado 2022

Single Cell Transcriptomics Reconstructs Fate Conversion from Fibroblast to Cardiomyocyte

por Liu, Ziqing, Wang, Li, Welch, Joshua D., Ma, Hong, Zhou, Yang, Vaseghi, Haley Ruth, Yu, Shuo, Wall, Joseph Blake, Alimohamadi, Sahar, Zheng, Michael, Yin, Chaoying, Shen, Weining, Prins, Jan F., Liu, Jiandong, Qian, Li
Publicado 2017

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

por Wang, Kai, Singh, Darshan, Zeng, Zheng, Coleman, Stephen J., Huang, Yan, Savich, Gleb L., He, Xiaping, Mieczkowski, Piotr, Grimm, Sara A., Perou, Charles M., MacLeod, James N., Chiang, Derek Y., Prins, Jan F., Liu, Jinze
Publicado 2010

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects

por Simon, Jeremy M., Hacker, Kathryn E., Singh, Darshan, Brannon, A. Rose, Parker, Joel S., Weiser, Matthew, Ho, Thai H., Kuan, Pei-Fen, Jonasch, Eric, Furey, Terrence S., Prins, Jan F., Lieb, Jason D., Rathmell, W. Kimryn, Davis, Ian J.
Publicado 2014

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq

por Hu, Yin, Huang, Yan, Du, Ying, Orellana, Christian F., Singh, Darshan, Johnson, Amy R., Monroy, Anaïs, Kuan, Pei-Fen, Hammond, Scott M., Makowski, Liza, Randell, Scott H., Chiang, Derek Y., Hayes, D. Neil, Jones, Corbin, Liu, Yufeng, Prins, Jan F., Liu, Jinze
Publicado 2013