Cache-Aware Asymptotically-Optimal Sampling-Based Motion Planning

door Ichnowski, Jeffrey, Prins, Jan F., Alterovitz, Ron
Gepubliceerd in IEEE Int Conf Robot Autom (2014)

Robust detection of alternative splicing in a population of single cells

door Welch, Joshua D., Hu, Yin, Prins, Jan F.
Gepubliceerd in Nucleic Acids Res (2016)

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

door Welch, Joshua D., Hartemink, Alexander J., Prins, Jan F.
Gepubliceerd in Genome Biol (2016)

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

door Welch, Joshua D., Hartemink, Alexander J., Prins, Jan F.
Gepubliceerd in Genome Biol (2017)

A probabilistic framework for aligning paired-end RNA-seq data

door Hu, Yin, Wang, Kai, He, Xiaping, Chiang, Derek Y., Prins, Jan F., Liu, Jinze
Gepubliceerd in 2010

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

door Welch, Joshua D, Baran-Gale, Jeanette, Perou, Charles M, Sethupathy, Praveen, Prins, Jan F
Gepubliceerd in BMC Genomics (2015)

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

door Welch, Joshua D., Slevin, Michael K., Tatomer, Deirdre C., Duronio, Robert J., Prins, Jan F., Marzluff, William F.
Gepubliceerd in RNA (2015)

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

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

A Robust Method for Transcript Quantification with RNA-Seq Data

door Huang, Yan, Hu, Yin, Jones, Corbin D., MacLeod, James N., Chiang, Derek Y., Liu, Yufeng, Prins, Jan F., Liu, Jinze
Gepubliceerd in 2013

BlackOPs: increasing confidence in variant detection through mappability filtering

door 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
Gepubliceerd in 2013

Deep sequencing shows multiple oligouridylations are required for 3′ to 5′ degradation of histone mRNAs on polyribosomes

door Slevin, Michael K., Meaux, Stacie, Welch, Joshua D., Bigler, Rebecca, Miliani de Marval, Paula L., Su, Wei, Rhoads, Robert E., Prins, Jan F., Marzluff, William F.
Gepubliceerd in Mol Cell (2014)

Single Cell Transcriptomic Analyses of Cell Fate Transitions during Human Cardiac Reprogramming

door Zhou, Yang, Liu, Ziqing, Welch, Joshua D., Gao, Xu, Wang, Li, Garbutt, Tiffany, Keepers, Benjamin, Ma, Hong, Prins, Jan F., Shen, Weining, Liu, Jiandong, Qian, Li
Gepubliceerd in Cell Stem Cell (2019)

Selective single cell isolation for genomics using microraft arrays

door 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.
Gepubliceerd in Nucleic Acids Res (2016)

Single Cell Transcriptomics Reconstructs Fate Conversion from Fibroblast to Cardiomyocyte

door 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
Gepubliceerd in Nature (2017)

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

door 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
Gepubliceerd in 2010

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

door 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.
Gepubliceerd in 2014

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

door 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
Gepubliceerd in 2013

Integrated Genomic Characterization of Papillary Thyroid Carcinoma

door Agrawal, Nishant, Akbani, Rehan, Aksoy, B. Arman, Ally, Adrian, Arachchi, Harindra, Asa, Sylvia L., Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Baylin, Stephen B., Behera, Madhusmita, Bernard, Brady, Beroukhim, Rameen, Bishop, Justin A., Black, Aaron D., Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bowlby, Reanne, Bristow, Christopher A., Brookens, Robin, Brooks, Denise, Bryant, Robert, Buda, Elizabeth, Butterfield, Yaron S.N., Carling, Tobias, Carlsen, Rebecca, Carter, Scott L., Carty, Sally E., Chan, Timothy A., Chen, Amy Y., Cherniack, Andrew D., Cheung, Dorothy, Chin, Lynda, Cho, Juok, Chu, Andy, Chuah, Eric, Cibulskis, Kristian, Ciriello, Giovanni, Clarke, Amanda, Clayman, Gary L., Cope, Leslie, Copland, John, Covington, Kyle, Danilova, Ludmila, Davidsen, Tanja, Demchok, John A., DiCara, Daniel, Dhalla, Noreen, Dhir, Rajiv, Dookran, Sheliann S., Dresdner, Gideon, Eldridge, Jonathan, Eley, Greg, El-Naggar, Adel K., Eng, Stephanie, Fagin, James A., Fennell, Timothy, Ferris, Robert L., Fisher, Sheila, Frazer, Scott, Frick, Jessica, Gabriel, Stacey B., Ganly, Ian, Gao, Jianjiong, Garraway, Levi A., Gastier-Foster, Julie M., Getz, Gad, Gehlenborg, Nils, Ghossein, Ronald, Gibbs, Richard A., Giordano, Thomas J., Gomez-Hernandez, Karen, Grimsby, Jonna, Gross, Benjamin, Guin, Ranabir, Hadjipanayis, Angela, Harper, Hollie A., Hayes, D. Neil, Heiman, David I., Herman, James G., Hoadley, Katherine A., Hofree, Matan, Holt, Robert A., Hoyle, Alan P., Huang, Franklin W., Huang, Mei, Hutter, Carolyn M., Ideker, Trey, Iype, Lisa, Jacobsen, Anders, Jefferys, Stuart R., Jones, Corbin D., Jones, Steven J.M., Kasaian, Katayoon, Kebebew, Electron, Khuri, Fadlo R., Kim, Jaegil, Kramer, Roger, Kreisberg, Richard, Kucherlapati, Raju, Kwiatkowski, David J., Ladanyi, Marc, Lai, Phillip H., Laird, Peter W., Lander, Eric, Lawrence, Michael S., Lee, Darlene, Lee, Eunjung, Lee, Semin, Lee, William, Leraas, Kristen M., Lichtenberg, Tara M., Lichtenstein, Lee, Lin, Pei, Ling, Shiyun, Liu, Jinze, Liu, Wenbin, Liu, Yingchun, LiVolsi, Virginia A., Lu, Yiling, Ma, Yussanne, Mahadeshwar, Harshad S., Marra, Marco A., Mayo, Michael, McFadden, David G., Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, Michael, Mills, Gordon, Moore, Richard A., Mose, Lisle E., Mungall, Andrew J., Murray, Bradley A., Nikiforov, Yuri E., Noble, Michael S., Ojesina, Akinyemi I., Owonikoko, Taofeek K., Ozenberger, Bradley A., Pantazi, Angeliki, Parfenov, Michael, Park, Peter J., Parker, Joel S., Paull, Evan O., Pedamallu, Chandra Sekhar, Perou, Charles M., Prins, Jan F., Protopopov, Alexei, Ramalingam, Suresh S., Ramirez, Nilsa C., Ramirez, Ricardo, Raphael, Benjamin J., Rathmell, W. Kimryn, Ren, Xiaojia, Reynolds, Sheila M., Rheinbay, Esther, Ringel, Matthew D., Rivera, Michael, Roach, Jeffrey, Robertson, A. Gordon, Rosenberg, Mara W., Rosenthall, Matthew, Sadeghi, Sara, Saksena, Gordon, Sander, Chris, Santoso, Netty, Schein, Jacqueline E., Schultz, Nikolaus, Schumacher, Steven E., Seethala, Raja R., Seidman, Jonathan, Senbabaoglu, Yasin, Seth, Sahil, Sharpe, Samantha, Mills Shaw, Kenna R., Shen, John P., Shen, Ronglai, Sherman, Steven, Sheth, Margi, Shi, Yan, Shmulevich, Ilya, Sica, Gabriel L., Simons, Janae V., Sipahimalani, Payal, Smallridge, Robert C., Sofia, Heidi J., Soloway, Matthew G., Song, Xingzhi, Sougnez, Carrie, Stewart, Chip, Stojanov, Petar, Stuart, Joshua M., Tabak, Barbara, Tam, Angela, Tan, Donghui, Tang, Jiabin, Tarnuzzer, Roy, Taylor, Barry S., Thiessen, Nina, Thorne, Leigh, Thorsson, Vésteinn, Tuttle, R. Michael, Umbricht, Christopher B., Van Den Berg, David J., Vandin, Fabio, Veluvolu, Umadevi, Verhaak, Roel G.W., Vinco, Michelle, Voet, Doug, Walter, Vonn, Wang, Zhining, Waring, Scot, Weinberger, Paul M., Weinstein, John N., Weisenberger, Daniel J., Wheeler, David, Wilkerson, Matthew D., Wilson, Jocelyn, Williams, Michelle, Winer, Daniel A., Wise, Lisa, Wu, Junyuan, Xi, Liu, Xu, Andrew W., Yang, Liming, Yang, Lixing, Zack, Travis I., Zeiger, Martha A., Zeng, Dong, Zenklusen, Jean Claude, Zhao, Ni, Zhang, Hailei, Zhang, Jianhua, Zhang, Jiashan (Julia), Zhang, Wei, Zmuda, Erik, Zou., Lihua
Gepubliceerd in Cell (2014)

Characterization of HPV and host genome interactions in primary head and neck cancers

door Parfenov, Michael, Pedamallu, Chandra Sekhar, Gehlenborg, Nils, Freeman, Samuel S., Danilova, Ludmila, Bristow, Christopher A., Lee, Semin, Hadjipanayis, Angela G., Ivanova, Elena V., Wilkerson, Matthew D., Protopopov, Alexei, Yang, Lixing, Seth, Sahil, Song, Xingzhi, Tang, Jiabin, Ren, Xiaojia, Zhang, Jianhua, Pantazi, Angeliki, Santoso, Netty, Xu, Andrew W., Mahadeshwar, Harshad, Wheeler, David A., Haddad, Robert I., Jung, Joonil, Ojesina, Akinyemi I., Issaeva, Natalia, Yarbrough, Wendell G., Hayes, D. Neil, Grandis, Jennifer R., El-Naggar, Adel K., Meyerson, Matthew, Park, Peter J., Chin, Lynda, Seidman, J. G., Hammerman, Peter S., Kucherlapati, Raju, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Bowlby, Reanne, Butterfield, Yaron S.N., Carlsen, Rebecca, Cheng, Dean, Chu, Andy, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A., Jones, Steven J.M., Lee, Darlene, Li, Haiyan I., Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Robertson, A. Gordon, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Protopopov, Alexei, Santoso, Netty, Lee, Semin, Parfenov, Michael, Zhang, Jianhua, Mahadeshwar, Harshad S., Tang, Jiabin, Ren, Xiaojia, Seth, Sahil, Haseley, Psalm, Zeng, Dong, Yang, Lixing, Xu, Andrew W., Song, Xingzhi, Pantazi, Angeliki, Bristow, Christopher, Hadjipanayis, Angela, Seidman, Jonathan, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Akbani, Rehan, Casasent, Tod, Liu, Wenbin, Lu, Yiling, Mills, Gordon, Motter, Thomas, Weinstein, John, Diao, Lixia, Wang, Jing, Fan, You Hong, Liu, Jinze, Wang, Kai, Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Buda, Elizabeth, Hayes, D. Neil, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Kimes, Patrick K., Marron, J.S., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Parker, Joel S., Perou, Charles M., Prins, Jan F., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Singh, Darshan, Soloway, Mathew G., Tan, Donghui, Veluvolu, Umadevi, Walter, Vonn, Waring, Scot, Wilkerson, Matthew D., Wu, Junyuan, Zhao, Ni, Cherniack, Andrew D., Hammerman, Peter S., Tward, Aaron D., Pedamallu, Chandra Sekhar, Saksena, Gordon, Jung, Joonil, Ojesina, Akinyemi I., Carter, Scott L., Zack, Travis I., Schumacher, Steven E., Beroukhim, Rameen, Freeman, Samuel S., Meyerson, Matthew, Cho, Juok, Chin, Lynda, Getz, Gad, Noble, Michael S., DiCara, Daniel, Zhang, Hailei, Heiman, David I., Gehlenborg, Nils, Voet, Doug, Lin, Pei, Frazer, Scott, Stojanov, Petar, Liu, Yingchun, Zou, Lihua, Kim, Jaegil, Lawrence, Michael S., Sougnez, Carrie, Lichtenstein, Lee, Cibulskis, Kristian, Lander, Eric, Gabriel, Stacey B., Muzny, Donna, Doddapaneni, HarshaVardhan, Kovar, Christie, Reid, Jeff, Morton, Donna, Han, Yi, Hale, Walker, Chao, Hsu, Chang, Kyle, Drummond, Jennifer A., Gibbs, Richard A., Kakkar, Nipun, Wheeler, David, Xi, Liu, Ciriello, Giovanni, Ladanyi, Marc, Lee, William, Ramirez, Ricardo, Sander, Chris, Shen, Ronglai, Sinha, Rileen, Weinhold, Nils, Taylor, Barry S., Aksoy, B. Arman, Dresdner, Gideon, Gao, Jianjiong, Gross, Benjamin, Jacobsen, Anders, Reva, Boris, Schultz, Nikolaus, Sumer, S. Onur, Sun, Yichao, Chan, Timothy, Morris, Luc, Stuart, Joshua, Benz, Stephen, Ng, Sam, Benz, Christopher, Yau, Christina, Baylin, Stephen B., Cope, Leslie, Danilova, Ludmila, Herman, James G., Bootwalla, Moiz, Maglinte, Dennis T., Laird, Peter W., Triche, Timothy, Weisenberger, Daniel J., Van Den Berg, David J., Agrawal, Nishant, Bishop, Justin, Boutros, Paul C., Bruce, Jeff P, Byers, Lauren Averett, Califano, Joseph, Carey, Thomas E., Chen, Zhong, Cheng, Hui, Chiosea, Simion I., Cohen, Ezra, Diergaarde, Brenda, Egloff, Ann Marie, El-Naggar, Adel K., Ferris, Robert L., Frederick, Mitchell J., Grandis, Jennifer R., Guo, Yan, Haddad, Robert I., Hammerman, Peter S., Harris, Thomas, Hayes, D. Neil, Hui, Angela BY, Lee, J. Jack, Lippman, Scott M., Liu, Fei-Fei, McHugh, Jonathan B., Myers, Jeff, Ng, Patrick Kwok Shing, Perez-Ordonez, Bayardo, Pickering, Curtis R., Prystowsky, Michael, Romkes, Marjorie, Saleh, Anthony D., Sartor, Maureen A., Seethala, Raja, Seiwert, Tanguy Y., Si, Han, Tward, Aaron D., Van Waes, Carter, Waggott, Daryl M., Wiznerowicz, Maciej, Yarbrough, Wendell, Zhang, Jiexin, Zuo, Zhixiang, Burnett, Ken, Crain, Daniel, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candance, Shelton, Troy, Sherman, Mark, Yena, Peggy, Black, Aaron D., Bowen, Jay, Frick, Jessica, Gastier-Foster, Julie M., Harper, Hollie A., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Baboud, Julien, Jensen, Mark A., Kahn, Ari B., Pihl, Todd D., Pot, David A., Srinivasan, Deepak, Walton, Jessica S., Wan, Yunhu, Burton, Robert, Davidsen, Tanja, Demchok, John A., Eley, Greg, Ferguson, Martin L., Shaw, Kenna R. Mills, Ozenberger, Bradley A., Sheth, Margi, Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean Claude, Saller, Charles, Tarvin, Katherine, Chen, Chu, Bollag, Roni, Weinberger, Paul, Golusiński, Wojciech, Golusiński, Paweł, Ibbs, Matthiew, Korski, Konstanty, Mackiewicz, Andrzej, Suchorska, Wiktoria, Szybiak, Bartosz, Wiznerowicz, Maciej, Burnett, Ken, Curley, Erin, Gardner, Johanna, Mallery, David, Penny, Robert, Shelton, Troy, Yena, Peggy, Beard, Christina, Mitchell, Colleen, Sandusky, George, Agrawal, Nishant, Ahn, Julie, Bishop, Justin, Califano, Joseph, Khan, Zubair, Bruce, Jeff P, Hui, Angela BY, Irish, Jonathan, Liu, Fei-Fei, Perez-Ordonez, Bayardo, Waldron, John, Boutros, Paul C., Waggott, Daryl M., Myers, Jeff, Lippman, Scott M., Egea, Sophie, Gomez-Fernandez, Carmen, Herbert, Lynn, Bradford, Carol R., Carey, Thomas E., Chepeha, Douglas B., Haddad, Andrea S., Jones, Tamara R., Komarck, Christine M., Malakh, Mayya, McHugh, Jonathan B., Moyer, Jeffrey S., Nguyen, Ariane, Peterson, Lisa A., Prince, Mark E., Rozek, Laura S., Sartor, Maureen A., Taylor, Evan G., Walline, Heather M., Wolf, Gregory T., Boice, Lori, Chera, Bhishamjit S., Funkhouser, William K., Gulley, Margaret L., Hackman, Trevor G., Hayes, D. Neil, Hayward, Michele C., Huang, Mei, Rathmell, W. Kimryn, Salazar, Ashley H., Shockley, William W., Shores, Carol G., Thorne, Leigh, Weissler, Mark C., Wrenn, Sylvia, Zanation, Adam M., Chiosea, Simion I., Diergaarde, Brenda, Egloff, Ann Marie, Ferris, Robert L., Romkes, Marjorie, Seethala, Raja, Brown, Brandee T., Guo, Yan, Pham, Michelle, Yarbrough, Wendell G.
Gepubliceerd in 2014