Computational methods for DNA copy-number analysis of tumors

Por Kendall, Jude, Krasnitz, Alexander
Publicado no Methods Mol Biol (2014)

Early Detection of Cancer in Blood Using Single-Cell Analysis: a Proposal

Por Krasnitz, Alexander, Kendall, Jude, Alexander, Joan, Levy, Dan, Wigler, Michael
Publicado no Trends Mol Med (2017)

Interactive analysis and assessment of single-cell copy-number variations

Por Garvin, Tyler, Aboukhalil, Robert, Kendall, Jude, Baslan, Timour, Atwal, Gurinder S., Hicks, James, Wigler, Michael, Schatz, Michael C.
Publicado no Nat Methods (2015)

SMASH, a fragmentation and sequencing method for genomic copy number analysis

Por Wang, Zihua, Andrews, Peter, Kendall, Jude, Ma, Beicong, Hakker, Inessa, Rodgers, Linda, Ronemus, Michael, Wigler, Michael, Levy, Dan
Publicado no Genome Res (2016)

Updates to the RMAP short-read mapping software

Por Smith, Andrew D., Chung, Wen-Yu, Hodges, Emily, Kendall, Jude, Hannon, Greg, Hicks, James, Xuan, Zhenyu, Zhang, Michael Q.
Publicado em 2009

Oncogenic cooperation and coamplification of developmental transcription factor genes in lung cancer

Por Kendall, Jude, Liu, Qing, Bakleh, Amy, Krasnitz, Alex, Nguyen, Ken C. Q., Lakshmi, B., Gerald, William L., Powers, Scott, Mu, David
Publicado em 2007

Reducing system noise in copy number data using principal components of self-self hybridizations

Por Lee, Yoon-ha, Ronemus, Michael, Kendall, Jude, Lakshmi, B., Leotta, Anthony, Levy, Dan, Esposito, Diane, Grubor, Vladimir, Ye, Kenny, Wigler, Michael, Yamrom, Boris
Publicado em 2012

Rapid Phenotypic and Genomic Change in Response to Therapeutic Pressure in Prostate Cancer Inferred by High Content Analysis of Single Circulating Tumor Cells

Por Dago, Angel E., Stepansky, Asya, Carlsson, Anders, Luttgen, Madelyn, Kendall, Jude, Baslan, Timour, Kolatkar, Anand, Wigler, Michael, Bethel, Kelly, Gross, Mitchell E., Hicks, James, Kuhn, Peter
Publicado em 2014

Genome wide copy number analysis of single cells

Por Baslan, Timour, Kendall, Jude, Rodgers, Linda, Cox, Hilary, Riggs, Mike, Stepansky, Asya, Troge, Jennifer, Ravi, Kandasamy, Esposito, Diane, Lakshmi, B., Wigler, Michael, Navin, Nicholas, Hicks, James
Publicado no Nat Protoc (2012)

A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding

Por Floer, Monique, Wang, Xin, Prabhu, Vidya, Berrozpe, Georgina, Narayan, Santosh, Spagna, Dan, Alvarez, David, Kendall, Jude, Krasnitz, Alexander, Stepansky, Asya, Hicks, James, Bryant, Gene O., Ptashne, Mark
Publicado em 2010

Limited Genomic Heterogeneity of Circulating Melanoma Cells in Advanced Stage Patients

Por Ruiz, Carmen, Li, Julia, Luttgen, Madelyn S., Kolatkar, Anand, Kendall, Jude T., Flores, Edna, Topp, Zheng, Samlowski, Wolfram E., McClay, Ed, Bethel, Kelly, Ferrone, Soldano, Hicks, James, Kuhn, Peter
Publicado no Phys Biol (2015)

Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation

Por Kamalakaran, Sitharthan, Kendall, Jude, Zhao, Xiaoyue, Tang, Chunlao, Khan, Sohail, Ravi, Kandasamy, Auletta, Theresa, Riggs, Michael, Wang, Yun, Helland, Åslaug, Naume, Bjørn, Dimitrova, Nevenka, Børresen-Dale, Anne-Lise, Hicks, Jim, Lucito, Robert
Publicado em 2009

Inferring tumor progression from genomic heterogeneity

Por Navin, Nicholas, Krasnitz, Alexander, Rodgers, Linda, Cook, Kerry, Meth, Jennifer, Kendall, Jude, Riggs, Michael, Eberling, Yvonne, Troge, Jennifer, Grubor, Vladimir, Levy, Dan, Lundin, Pär, Månér, Susanne, Zetterberg, Anders, Hicks, James, Wigler, Michael
Publicado em 2010

Tumor Evolution Inferred by Single Cell Sequencing

Por Navin, Nicholas, Kendall, Jude, Troge, Jennifer, Andrews, Peter, Rodgers, Linda, McIndoo, Jeanne, Cook, Kerry, Stepansky, Asya, Levy, Dan, Esposito, Diane, Muthuswamy, Lakshmi, Krasnitz, Alex, McCombie, Richard, Hicks, James, Wigler, Michael
Publicado no Nature (2011)

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

Por Hodges, Emily, Smith, Andrew D., Kendall, Jude, Xuan, Zhenyu, Ravi, Kandasamy, Rooks, Michelle, Zhang, Michael Q., Ye, Kenny, Bhattacharjee, Arindam, Brizuela, Leonardo, McCombie, W. Richard, Wigler, Michael, Hannon, Gregory J., Hicks, James B.
Publicado em 2009

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

Por Regulski, Michael, Lu, Zhenyuan, Kendall, Jude, Donoghue, Mark T.A., Reinders, Jon, Llaca, Victor, Deschamps, Stephane, Smith, Andrew, Levy, Dan, McCombie, W. Richard, Tingey, Scott, Rafalski, Antoni, Hicks, James, Ware, Doreen, Martienssen, Robert A.
Publicado em 2013

The contribution of de novo and rare inherited copy number changes to congenital heart disease in an unselected sample of children with conotruncal defects or hypoplastic left hear...

Por Warburton, Dorothy, Ronemus, Michael, Kline, Jennie, Jobanputra, Vaidehi, Williams, Ismee, Anyane-Yeboa, Kwame, Chung, Wendy, Yu, Lan, Wong, Nancy, Awad, Danielle, Yu, Chih-yu, Leotta, Anthony, Kendall, Jude, Yamrom, Boris, Lee, Yoon-ha, Wigler, Michael, Levy, Dan
Publicado em 2013

Optimizing sparse sequencing of single cells for highly multiplex copy number profiling

Por Baslan, Timour, Kendall, Jude, Ward, Brian, Cox, Hilary, Leotta, Anthony, Rodgers, Linda, Riggs, Michael, D'Italia, Sean, Sun, Guoli, Yong, Mao, Miskimen, Kristy, Gilmore, Hannah, Saborowski, Michael, Dimitrova, Nevenka, Krasnitz, Alexander, Harris, Lyndsay, Wigler, Michael, Hicks, James
Publicado no Genome Res (2015)

TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24− cancer cells

Por Pal, Debjani, Pertot, Anja, Shirole, Nitin H, Yao, Zhan, Anaparthy, Naishitha, Garvin, Tyler, Cox, Hilary, Chang, Kenneth, Rollins, Fred, Kendall, Jude, Edwards, Leyla, Singh, Vijay A, Stone, Gary C, Schatz, Michael C, Hicks, James, Hannon, Gregory J, Sordella, Raffaella
Publicado no eLife (2017)

Rare De Novo Germline Copy-Number Variation in Testicular Cancer

Por Stadler, Zsofia K., Esposito, Diane, Shah, Sohela, Vijai, Joseph, Yamrom, Boris, Levy, Dan, Lee, Yoon-ha, Kendall, Jude, Leotta, Anthony, Ronemus, Michael, Hansen, Nichole, Sarrel, Kara, Rau-Murthy, Rohini, Schrader, Kasmintan, Kauff, Noah, Klein, Robert J., Lipkin, Steven M., Murali, Rajmohan, Robson, Mark, Sheinfeld, Joel, Feldman, Darren, Bosl, George, Norton, Larry, Wigler, Michael, Offit, Kenneth
Publicado em 2012