R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R

Autor Ramaker, Ryne C, Gordon, Emily R, Cooper, Sara J
Vydáno v Bioinformatics (2018)

CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries

Autor Hardigan, Andrew A, Roberts, Brian S, Moore, Dianna E, Ramaker, Ryne C, Jones, Angela L, Myers, Richard M
Vydáno v Nucleic Acids Res (2019)

Pooled CRISPR screening in pancreatic cancer cells implicates co-repressor complexes as a cause of multiple drug resistance via regulation of epithelial-to-mesenchymal transition

Autor Ramaker, Ryne C., Hardigan, Andrew A., Gordon, Emily R., Wright, Carter A., Myers, Richard M., Cooper, Sara J.
Vydáno v BMC Cancer (2021)

RNA sequencing-based cell proliferation analysis across 19 cancers identifies a subset of proliferation-informative cancers with a common survival signature

Autor Ramaker, Ryne C., Lasseigne, Brittany N., Hardigan, Andrew A., Palacio, Laura, Gunther, David S., Myers, Richard M., Cooper, Sara J.
Vydáno v Oncotarget (2017)

A genome-wide interactome of DNA-associated proteins in the human liver

Autor Ramaker, Ryne C., Savic, Daniel, Hardigan, Andrew A., Newberry, Kimberly, Cooper, Gregory M., Myers, Richard M., Cooper, Sara J.
Vydáno v Genome Res (2017)

Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations

Autor Ramaker, Ryne C., Hardigan, Andrew A., Goh, Say-Tar, Partridge, E. Christopher, Wold, Barbara, Cooper, Sara J., Myers, Richard M.
Vydáno v Genome Res (2020)

Differential stress induced c-Fos expression and identification of region-specific miRNA-mRNA networks in the dorsal raphe and amygdala of high-responder/low-responder rats

Autor Cohen, Joshua L., Ata, Anooshah E., Jackson, Nateka L., Rahn, Elizabeth J., Ramaker, Ryne C., Cooper, Sara, Kerman, Ilan A., Clinton, Sarah M.
Vydáno v Behav Brain Res (2016)

Distinct gene regulatory programs define the inhibitory effects of liver X receptors and PPARG on cancer cell proliferation

Autor Savic, Daniel, Ramaker, Ryne C., Roberts, Brian S., Dean, Emma C., Burwell, Todd C., Meadows, Sarah K., Cooper, Sara J., Garabedian, Michael J., Gertz, Jason, Myers, Richard M.
Vydáno v Genome Med (2016)

aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments

Autor Alonso, Arnald, Lasseigne, Brittany N, Williams, Kelly, Nielsen, Josh, Ramaker, Ryne C, Hardigan, Andrew A, Johnston, Bobbi, Roberts, Brian S, Cooper, Sara J, Marsal, Sara, Myers, Richard M
Vydáno v Bioinformatics (2017)

Discovery and validation of circulating biomarkers of colorectal adenoma by high-depth small RNA sequencing

Autor Roberts, Brian S., Hardigan, Andrew A., Moore, Dianna E., Ramaker, Ryne C., Jones, Angela L., Fitz-Gerald, Meredith B., Cooper, Gregory M., Wilcox, C. Mel, Kimberly, Robert P., Myers, Richard M.
Vydáno v Clin Cancer Res (2018)

Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns

Autor Kirby, Marie K., Ramaker, Ryne C., Roberts, Brian S., Lasseigne, Brittany N., Gunther, David S., Burwell, Todd C., Davis, Nicholas S., Gulzar, Zulfiqar G., Absher, Devin M., Cooper, Sara J., Brooks, James D., Myers, Richard M.
Vydáno v BMC Cancer (2017)

Kinase Gene Expression Profiling of Metastatic Clear Cell Renal Cell Carcinoma Tissue Identifies Potential New Therapeutic Targets

Autor Ghatalia, Pooja, Yang, Eddy S., Lasseigne, Brittany N., Ramaker, Ryne C., Cooper, Sara J., Chen, Dongquan, Sudarshan, Sunil, Wei, Shi, Guru, Arjun S., Zhao, Amy, Cooper, Tiffiny, Della Manna, Deborah L., Naik, Gurudatta, Myers, Richard M., Sonpavde, Guru
Vydáno v PLoS One (2016)

RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long‐term survival and reveals a role for ANGPTL4

Autor Kirby, Marie K., Ramaker, Ryne C., Gertz, Jason, Davis, Nicholas S., Johnston, Bobbi E., Oliver, Patsy G., Sexton, Katherine C., Greeno, Edward W., Christein, John D., Heslin, Martin J., Posey, James A., Grizzle, William E., Vickers, Selwyn M., Buchsbaum, Donald J., Cooper, Sara J., Myers, Richard M.
Vydáno v Mol Oncol (2016)

Long-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders

Autor Hiatt, Susan M., Lawlor, James M.J., Handley, Lori H., Ramaker, Ryne C., Rogers, Brianne B., Partridge, E. Christopher, Boston, Lori Beth, Williams, Melissa, Plott, Christopher B., Jenkins, Jerry, Gray, David E., Holt, James M., Bowling, Kevin M., Bebin, E. Martina, Grimwood, Jane, Schmutz, Jeremy, Cooper, Gregory M.
Vydáno v HGG Adv (2021)

Occupancy maps of 208 chromatin-associated proteins in one human cell type

Autor Partridge, E. Christopher, Chhetri, Surya B., Prokop, Jeremy W., Ramaker, Ryne C., Jansen, Camden S., Goh, Say-Tar, Mackiewicz, Mark, Newberry, Kimberly M., Brandsmeier, Laurel A., Meadows, Sarah K., Messer, C. Luke, Hardigan, Andrew A., Coppola, Candice J., Dean, Emma C., Jiang, Shan, Savic, Daniel, Mortazavi, Ali, Wold, Barbara J., Myers, Richard M., Mendenhall, Eric M.
Vydáno v Nature (2020)

Post-mortem molecular profiling of three psychiatric disorders

Autor Ramaker, Ryne C., Bowling, Kevin M., Lasseigne, Brittany N., Hagenauer, Megan H., Hardigan, Andrew A., Davis, Nicholas S., Gertz, Jason, Cartagena, Preston M., Walsh, David M., Vawter, Marquis P., Jones, Edward G., Schatzberg, Alan F., Barchas, Jack D., Watson, Stanley J., Bunney, Blynn G., Akil, Huda, Bunney, William E., Li, Jun Z., Cooper, Sara J., Myers, Richard M.
Vydáno v Genome Med (2017)

Genomic regulation of invasion by STAT3 in triple negative breast cancer

Autor McDaniel, Joy M., Varley, Katherine E., Gertz, Jason, Savic, Daniel S., Roberts, Brian S., Bailey, Sarah K., Shevde, Lalita A., Ramaker, Ryne C., Lasseigne, Brittany N., Kirby, Marie K., Newberry, Kimberly M., Christopher Partridge, E ., Jones, Angela L., Boone, Braden, Levy, Shawn E., Oliver, Patsy G., Sexton, Katherine C., Grizzle, William E., Forero, Andres, Buchsbaum, Donald J., Cooper, Sara J., Myers, Richard M.
Vydáno v Oncotarget (2016)

De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay

Autor Hiatt, Susan M., Neu, Matthew B., Ramaker, Ryne C., Hardigan, Andrew A., Prokop, Jeremy W., Hancarova, Miroslava, Prchalova, Darina, Havlovicova, Marketa, Prchal, Jan, Stranecky, Viktor, Yim, Dwight K. C., Powis, Zöe, Keren, Boris, Nava, Caroline, Mignot, Cyril, Rio, Marlene, Revah-Politi, Anya, Hemati, Parisa, Stong, Nicholas, Iglesias, Alejandro D., Suchy, Sharon F., Willaert, Rebecca, Wentzensen, Ingrid M., Wheeler, Patricia G., Brick, Lauren, Kozenko, Mariya, Hurst, Anna C. E., Wheless, James W., Lacassie, Yves, Myers, Richard M., Barsh, Gregory S., Sedlacek, Zdenek, Cooper, Gregory M.
Vydáno v PLoS Genet (2018)