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

Por Ramaker, Ryne C, Gordon, Emily R, Cooper, Sara J
Publicado no Bioinformatics (2018)

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

Por Hardigan, Andrew A, Roberts, Brian S, Moore, Dianna E, Ramaker, Ryne C, Jones, Angela L, Myers, Richard M
Publicado no Nucleic Acids Res (2019)

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

Por Ramaker, Ryne C., Lasseigne, Brittany N., Hardigan, Andrew A., Palacio, Laura, Gunther, David S., Myers, Richard M., Cooper, Sara J.
Publicado no Oncotarget (2017)

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

Por Ramaker, Ryne C., Savic, Daniel, Hardigan, Andrew A., Newberry, Kimberly, Cooper, Gregory M., Myers, Richard M., Cooper, Sara J.
Publicado no Genome Res (2017)

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

Por Ramaker, Ryne C., Hardigan, Andrew A., Goh, Say-Tar, Partridge, E. Christopher, Wold, Barbara, Cooper, Sara J., Myers, Richard M.
Publicado no 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

Por Cohen, Joshua L., Ata, Anooshah E., Jackson, Nateka L., Rahn, Elizabeth J., Ramaker, Ryne C., Cooper, Sara, Kerman, Ilan A., Clinton, Sarah M.
Publicado no Behav Brain Res (2016)

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

Por 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.
Publicado no Genome Med (2016)

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

Por 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
Publicado no Bioinformatics (2017)

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

Por 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.
Publicado no Clin Cancer Res (2018)

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

Por 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.
Publicado no BMC Cancer (2017)

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

Por 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
Publicado no PLoS One (2016)

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

Por 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.
Publicado no Mol Oncol (2016)

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

Por 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.
Publicado no Nature (2020)

Post-mortem molecular profiling of three psychiatric disorders

Por 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.
Publicado no Genome Med (2017)

Genomic regulation of invasion by STAT3 in triple negative breast cancer

Por 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.
Publicado no Oncotarget (2016)

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

Por 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.
Publicado no PLoS Genet (2018)