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)

Integrated Computational Pipeline for Single-Cell Genomic Profiling

Por Chorbadjiev, Lubomir, Kendall, Jude, Alexander, Joan, Zhygulin, Viacheslav, Song, Junyan, Wigler, Michael, Krasnitz, Alexander
Publicado no JCO Clin Cancer Inform (2020)

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)

Single chromosomal gains can function as metastasis suppressors and promoters in colon cancer

Por Vasudevan, Anand, Baruah, Prasamit S., Smith, Joan C., Wang, Zihua, Sayles, Nicole M., Andrews, Peter, Kendall, Jude, Leu, Justin, Chunduri, Narendra Kumar, Levy, Dan, Wigler, Michael, Storchová, Zuzana, Sheltzer, Jason M.
Publicado no Dev Cell (2020)

Multiplex accurate sensitive quantitation (MASQ) with application to minimal residual disease in acute myeloid leukemia

Por Moffitt, Andrea B, Spector, Mona S, Andrews, Peter, Kendall, Jude, Alexander, Joan, Stepansky, Asya, Ma, BeiCong, Kolitz, Jonathan, Chiorazzi, Nicholas, Allen, Steven L, Krasnitz, Alex, Wigler, Michael, Levy, Dan, Wang, Zihua
Publicado no Nucleic Acids Res (2020)

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

Copy number alterations in pancreatic cancer identify recurrent PAK4 amplification

Por Chen, Shuaili, Auletta, Theresa, Dovirak, Ostap, Hutter, Christina, Kuntz, Karen, El-ftesi, Samira, Kendall, Jude, Han, Haiyong, Von Hoff, Daniel D., Ashfaq, Raheela, Maitra, Anirban, Iacobuzio-Donahue, Christine A., Hruban, Ralph H., Lucito, Robert
Publicado no Cancer Biol Ther (2008)

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