Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud

por Griffith, Malachi, Walker, Jason R., Spies, Nicholas C., Ainscough, Benjamin J., Griffith, Obi L.
Publicado en PLoS Comput Biol (2015)

DGIdb 3.0: a redesign and expansion of the drug–gene interaction database

por Cotto, Kelsy C, Wagner, Alex H, Feng, Yang-Yang, Kiwala, Susanna, Coffman, Adam C, Spies, Gregory, Wollam, Alex, Spies, Nicholas C, Griffith, Obi L, Griffith, Malachi
Publicado en Nucleic Acids Res (2018)

DGIdb 2.0: mining clinically relevant drug–gene interactions

por Wagner, Alex H., Coffman, Adam C., Ainscough, Benjamin J., Spies, Nicholas C., Skidmore, Zachary L., Campbell, Katie M., Krysiak, Kilannin, Pan, Deng, McMichael, Joshua F., Eldred, James M., Walker, Jason R., Wilson, Richard K., Mardis, Elaine R., Griffith, Malachi, Griffith, Obi L.
Publicado en Nucleic Acids Res (2016)

A phase 1 trial of BKM120 (Buparlisib) in combination with fulvestrant in postmenopausal women with estrogen receptor positive metastatic breast cancer

por Ma, Cynthia X., Luo, Jingqin, Naughton, Michael, Ademuyiwa, Foluso, Suresh, Rama, Griffith, Malachi, Griffith, Obi L., Skidmore, Zachary L., Spies, Nicholas C., Ramu, Avinash, Trani, Lee, Pluard, Timothy, Nagaraj, Gayathri, Thomas, Shana, Guo, Zhanfang, Hoog, Jeremy, Han, Jing, Mardis, Elaine, Lockhart, Craig, Ellis, Matthew J.
Publicado en Clin Cancer Res (2015)

Open-Sourced CIViC Annotation Pipeline to Identify and Annotate Clinically Relevant Variants Using Single-Molecule Molecular Inversion Probes

por Barnell, Erica K., Waalkes, Adam, Mosior, Matt C., Penewit, Kelsi, Cotto, Kelsy C., Danos, Arpad M., Sheta, Lana M., Campbell, Katie M., Krysiak, Kilannin, Rieke, Damian, Spies, Nicholas C., Skidmore, Zachary L., Pritchard, Colin C., Fehniger, Todd A., Uppaluri, Ravindra, Govindan, Ramaswamy, Griffith, Malachi, Salipante, Stephen J., Griffith, Obi L.
Publicado en JCO Clin Cancer Inform (2019)

DGIdb - Mining the druggable genome

por Griffith, Malachi, Griffith, Obi L., Coffman, Adam C., Weible, James V., McMichael, Josh F., Spies, Nicholas C., Koval, James, Das, Indraniel, Callaway, Matthew B., Eldred, James M., Miller, Christopher A., Subramanian, Janakiraman, Govindan, Ramaswamy, Kumar, Runjun D., Bose, Ron, Ding, Li, Walker, Jason R., Larson, David E., Dooling, David J., Smith, Scott M., Ley, Timothy J., Mardis, Elaine R., Wilson, Richard K.
Publicado 2013

Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples

por Barnell, Erica K., Ronning, Peter, Campbell, Katie M., Krysiak, Kilannin, Ainscough, Benjamin J., Sheta, Lana M., Pema, Shahil P., Schmidt, Alina D., Richters, Megan, Cotto, Kelsy C., Danos, Arpad M., Ramirez, Cody, Skidmore, Zachary L., Spies, Nicholas C., Hundal, Jasreet, Sediqzad, Malik S., Kunisaki, Jason, Gomez, Felicia, Trani, Lee, Matlock, Matthew, Wagner, Alex H., Swamidass, S. Joshua, Griffith, Malachi, Griffith, Obi L.
Publicado en Genet Med (2018)

Standard operating procedure for curation and clinical interpretation of variants in cancer

por Danos, Arpad M., Krysiak, Kilannin, Barnell, Erica K., Coffman, Adam C., McMichael, Joshua F., Kiwala, Susanna, Spies, Nicholas C., Sheta, Lana M., Pema, Shahil P., Kujan, Lynzey, Clark, Kaitlin A., Wollam, Amber Z., Rao, Shruti, Ritter, Deborah I., Sonkin, Dmitriy, Raca, Gordana, Lin, Wan-Hsin, Grisdale, Cameron J., Kim, Raymond H., Wagner, Alex H., Madhavan, Subha, Griffith, Malachi, Griffith, Obi L.
Publicado en Genome Med (2019)

NeoPalAna: Neoadjuvant palbociclib, a cyclin-dependent kinase 4/6 inhibitor, and anastrozole for clinical stage 2 or 3 estrogen receptor positive breast cancer

por Ma, Cynthia X., Gao, Feng, Luo, Jingqin, Northfelt, Donald W., Goetz, Matthew, Forero, Andres, Hoog, Jeremy, Naughton, Michael, Ademuyiwa, Foluso, Suresh, Rama, Anderson, Karen S., Margenthaler, Julie, Aft, Rebecca, Hobday, Timothy, Moynihan, Timothy, Gillanders, William, Cyr, Amy, Eberlein, Timothy J., Hieken, Tina, Krontiras, Helen, Guo, Zhanfang, Lee, Michelle V., Spies, Nicholas C., Skidmore, Zachary L., Griffith, Obi L., Griffith, Malachi, Thomas, Shana, Bumb, Caroline, Vij, Kiran, Bartlett, Cynthia Huang, Koehler, Maria, Al-Kateb, Hussam, Sanati, Souzan, Ellis, Matthew J.
Publicado en Clin Cancer Res (2017)

The prognostic effects of somatic mutations in ER-positive breast cancer

por Griffith, Obi L., Spies, Nicholas C., Anurag, Meenakshi, Griffith, Malachi, Luo, Jingqin, Tu, Dongsheng, Yeo, Belinda, Kunisaki, Jason, Miller, Christopher A, Krysiak, Kilannin, Hundal, Jasreet, Ainscough, Benjamin J, Skidmore, Zachary L., Campbell, Katie, Kumar, Runjun, Fronick, Catrina, Cook, Lisa, Snider, Jacqueline E., Davies, Sherri, Kavuri, Shyam M., Chang, Eric C., Magrini, Vincent, Larson, David E., Fulton, Robert S, Liu, Shuzhen, Leung, Samuel, Voduc, David, Bose, Ron, Dowsett, Mitch, Wilson, Richard K., Nielsen, Torsten O., Mardis, Elaine R, Ellis, Matthew J.
Publicado en Nat Commun (2018)

Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer

por Wagner, Alex H., Devarakonda, Siddhartha, Skidmore, Zachary L., Krysiak, Kilannin, Ramu, Avinash, Trani, Lee, Kunisaki, Jason, Masood, Ashiq, Waqar, Saiama N., Spies, Nicholas C., Morgensztern, Daniel, Waligorski, Jason, Ponce, Jennifer, Fulton, Robert S., Maggi, Leonard B., Weber, Jason D., Watson, Mark A., O’Conor, Christopher J., Ritter, Jon H., Olsen, Rachelle R., Cheng, Haixia, Mukhopadhyay, Anandaroop, Can, Ismail, Cessna, Melissa H., Oliver, Trudy G., Mardis, Elaine R., Wilson, Richard K., Griffith, Malachi, Griffith, Obi L., Govindan, Ramaswamy
Publicado en Nat Commun (2018)

Author Correction: The prognostic effects of somatic mutations in ER-positive breast cancer

por Griffith, Obi L., Spies, Nicholas C., Anurag, Meenakshi, Griffith, Malachi, Luo, Jingqin, Tu, Dongsheng, Yeo, Belinda, Kunisaki, Jason, Miller, Christopher A, Krysiak, Kilannin, Hundal, Jasreet, Ainscough, Benjamin J, Skidmore, Zachary L., Campbell, Katie, Kumar, Runjun, Fronick, Catrina, Cook, Lisa, Snider, Jacqueline E., Davies, Sherri, Kavuri, Shyam M., Chang, Eric C., Magrini, Vincent, Larson, David E., Fulton, Robert S, Liu, Shuzhen, Leung, Samuel, Voduc, David, Bose, Ron, Dowsett, Mitch, Wilson, Richard K., Nielsen, Torsten O., Mardis, Elaine R, Ellis, Matthew J.
Publicado en Nat Commun (2018)

Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B lymphoblastic leukemia

por Griffith, Malachi, Griffith, Obi L., Krysiak, Kilannin, Skidmore, Zachary L., Christopher, Matthew J., Klco, Jeffery M., Ramu, Avinash, Lamprecht, Tamara L., Wagner, Alex H., Campbell, Katie M., Lesurf, Robert, Hundal, Jasreet, Zhang, Jin, Spies, Nicholas C., Ainscough, Benjamin J., Larson, David E., Heath, Sharon E., Fronick, Catrina, O'Laughlin, Shelly, Fulton, Robert, Magrini, Vincent, McGrath, Sean, Smith, Scott M., Miller, Christopher A., Maher, Christopher A., Payton, Jacqueline E., Walker, Jason R., Eldred, James M., Walter, Matthew J., Link, Daniel C., Graubert, Timothy A., Westervelt, Peter, Kulkarni, Shashikant, DiPersio, John F., Mardis, Elaine R., Wilson, Richard K., Ley, Timothy J.
Publicado en Exp Hematol (2016)

Neoadjuvant and Adjuvant Pembrolizumab in Resectable Locally Advanced, Human Papillomavirus-Unrelated Head and Neck Cancer: A Multicenter, Phase 2 Trial

por Uppaluri, Ravindra, Campbell, Katie M., Egloff, Ann Marie, Zolkind, Paul, Skidmore, Zachary L., Nussenbaum, Brian, Paniello, Randal C., Rich, Jason T., Jackson, Ryan, Pipkorn, Patrik, Michel, Loren P., Ley, Jessica, Oppelt, Peter, Dunn, Gavin P., Barnell, Erica K., Spies, Nicholas C., Lin, Tianxiang, Li, Tiantian, Mulder, David T., Hanna, Youstina, Cirlan, Iulia, Pugh, Trevor J., Mudianto, Tenny, Riley, Rachel, Zhou, Liye, Jo, Vickie, Stachler, Matthew, Hanna, Glenn J., Kass, Jason, Haddad, Robert, Schoenfeld, Jonathan D., Gjini, Evisa, Lako, Ana, Thorstad, Wade, Gay, Hiram A., Daly, Mackenzie, Rodig, Scott J., Hagemann, Ian S., Kallogjeri, Dorina, Piccirillo, Jay F., Chernock, Rebecca D., Griffith, Malachi, Griffith, Obi L., Adkins, Douglas R.
Publicado en Clin Cancer Res (2020)

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

por Griffith, Malachi, Spies, Nicholas C, Krysiak, Kilannin, McMichael, Joshua F, Coffman, Adam C, Danos, Arpad M, Ainscough, Benjamin J, Ramirez, Cody A, Rieke, Damian T, Kujan, Lynzey, Barnell, Erica K, Wagner, Alex H, Skidmore, Zachary L, Wollam, Amber, Liu, Connor J, Jones, Martin R, Bilski, Rachel L, Lesurf, Robert, Feng, Yan-Yang, Shah, Nakul M, Bonakdar, Melika, Trani, Lee, Matlock, Matthew, Ramu, Avinash, Campbell, Katie M, Spies, Gregory C, Graubert, Aaron P, Gangavarapu, Karthik, Eldred, James M, Larson, David E, Walker, Jason R, Good, Benjamin M, Wu, Chunlei, Su, Andrew I, Dienstmann, Rodrigo, Margolin, Adam A, Tamborero, David, Lopez-Bigas, Nuria, Jones, Steven J M, Bose, Ron, Spencer, David H, Wartman, Lukas D, Wilson, Richard K, Mardis, Elaine R, Griffith, Obi L
Publicado en Nat Genet (2017)

Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element

por Leung, Wilson, Shaffer, Christopher D., Chen, Elizabeth J., Quisenberry, Thomas J., Ko, Kevin, Braverman, John M., Giarla, Thomas C., Mortimer, Nathan T., Reed, Laura K., Smith, Sheryl T., Robic, Srebrenka, McCartha, Shannon R., Perry, Danielle R., Prescod, Lindsay M., Sheppard, Zenyth A., Saville, Ken J., McClish, Allison, Morlock, Emily A., Sochor, Victoria R., Stanton, Brittney, Veysey-White, Isaac C., Revie, Dennis, Jimenez, Luis A., Palomino, Jennifer J., Patao, Melissa D., Patao, Shane M., Himelblau, Edward T., Campbell, Jaclyn D., Hertz, Alexandra L., McEvilly, Maddison F., Wagner, Allison R., Youngblom, James, Bedi, Baljit, Bettincourt, Jeffery, Duso, Erin, Her, Maiye, Hilton, William, House, Samantha, Karimi, Masud, Kumimoto, Kevin, Lee, Rebekah, Lopez, Darryl, Odisho, George, Prasad, Ricky, Robbins, Holly Lyn, Sandhu, Tanveer, Selfridge, Tracy, Tsukashima, Kara, Yosif, Hani, Kokan, Nighat P., Britt, Latia, Zoellner, Alycia, Spana, Eric P., Chlebina, Ben T., Chong, Insun, Friedman, Harrison, Mammo, Danny A., Ng, Chun L., Nikam, Vinayak S., Schwartz, Nicholas U., Xu, Thomas Q., Burg, Martin G., Batten, Spencer M., Corbeill, Lindsay M., Enoch, Erica, Ensign, Jesse J., Franks, Mary E., Haiker, Breanna, Ingles, Judith A., Kirkland, Lyndsay D., Lorenz-Guertin, Joshua M., Matthews, Jordan, Mittig, Cody M., Monsma, Nicholaus, Olson, Katherine J., Perez-Aragon, Guillermo, Ramic, Alen, Ramirez, Jordan R., Scheiber, Christopher, Schneider, Patrick A., Schultz, Devon E., Simon, Matthew, Spencer, Eric, Wernette, Adam C., Wykle, Maxine E., Zavala-Arellano, Elizabeth, McDonald, Mitchell J., Ostby, Kristine, Wendland, Peter, DiAngelo, Justin R., Ceasrine, Alexis M., Cox, Amanda H., Docherty, James E.B., Gingras, Robert M., Grieb, Stephanie M., Pavia, Michael J., Personius, Casey L., Polak, Grzegorz L., Beach, Dale L., Cerritos, Heaven L., Horansky, Edward A., Sharif, Karim A., Moran, Ryan, Parrish, Susan, Bickford, Kirsten, Bland, Jennifer, Broussard, Juliana, Campbell, Kerry, Deibel, Katelynn E., Forka, Richard, Lemke, Monika C., Nelson, Marlee B., O'Keeffe, Catherine, Ramey, S. Mariel, Schmidt, Luke, Villegas, Paola, Jones, Christopher J., Christ, Stephanie L., Mamari, Sami, Rinaldi, Adam S., Stity, Ghazal, Hark, Amy T., Scheuerman, Mark, Silver Key, S. Catherine, McRae, Briana D., Haberman, Adam S., Asinof, Sam, Carrington, Harriette, Drumm, Kelly, Embry, Terrance, McGuire, Richard, Miller-Foreman, Drew, Rosen, Stella, Safa, Nadia, Schultz, Darrin, Segal, Matt, Shevin, Yakov, Svoronos, Petros, Vuong, Tam, Skuse, Gary, Paetkau, Don W., Bridgman, Rachael K., Brown, Charlotte M., Carroll, Alicia R., Gifford, Francesca M., Gillespie, Julie Beth, Herman, Susan E., Holtcamp, Krystal L., Host, Misha A., Hussey, Gabrielle, Kramer, Danielle M., Lawrence, Joan Q., Martin, Madeline M., Niemiec, Ellen N., O'Reilly, Ashleigh P., Pahl, Olivia A., Quintana, Guadalupe, Rettie, Elizabeth A.S., Richardson, Torie L., Rodriguez, Arianne E., Rodriguez, Mona O., Schiraldi, Laura, Smith, Joanna J., Sugrue, Kelsey F., Suriano, Lindsey J., Takach, Kaitlyn E., Vasquez, Arielle M., Velez, Ximena, Villafuerte, Elizabeth J., Vives, Laura T., Zellmer, Victoria R., Hauke, Jeanette, Hauser, Charles R., Barker, Karolyn, Cannon, Laurie, Parsamian, Perouza, Parsons, Samantha, Wichman, Zachariah, Bazinet, Christopher W., Johnson, Diana E., Bangura, Abubakarr, Black, Jordan A., Chevee, Victoria, Einsteen, Sarah A., Hilton, Sarah K., Kollmer, Max, Nadendla, Rahul, Stamm, Joyce, Fafara-Thompson, Antoinette E., Gygi, Amber M., Ogawa, Emmy E., Van Camp, Matt, Kocsisova, Zuzana, Leatherman, Judith L., Modahl, Cassie M., Rubin, Michael R., Apiz-Saab, Susana S., Arias-Mejias, Suzette M., Carrion-Ortiz, Carlos F., Claudio-Vazquez, Patricia N., Espada-Green, Debbie M., Feliciano-Camacho, Marium, Gonzalez-Bonilla, Karina M., Taboas-Arroyo, Mariela, Vargas-Franco, Dorianmarie, Montañez-Gonzalez, Raquel, Perez-Otero, Joseph, Rivera-Burgos, Myrielis, Rivera-Rosario, Francisco J., Eisler, Heather L., Alexander, Jackie, Begley, Samatha K., Gabbard, Deana, Allen, Robert J., Aung, Wint Yan, Barshop, William D., Boozalis, Amanda, Chu, Vanessa P., Davis, Jeremy S., Duggal, Ryan N., Franklin, Robert, Gavinski, Katherine, Gebreyesus, Heran, Gong, Henry Z., Greenstein, Rachel A., Guo, Averill D., Hanson, Casey, Homa, Kaitlin E., Hsu, Simon C., Huang, Yi, Huo, Lucy, Jacobs, Sarah, Jia, Sasha, Jung, Kyle L., Wai-Chee Kong, Sarah, Kroll, Matthew R., Lee, Brandon M., Lee, Paul F., Levine, Kevin M., Li, Amy S., Liu, Chengyu, Liu, Max Mian, Lousararian, Adam P., Lowery, Peter B., Mallya, Allyson P., Marcus, Joseph E., Ng, Patrick C., Nguyen, Hien P., Patel, Ruchik, Precht, Hashini, Rastogi, Suchita, Sarezky, Jonathan M., Schefkind, Adam, Schultz, Michael B., Shen, Delia, Skorupa, Tara, Spies, Nicholas C., Stancu, Gabriel, Vivian Tsang, Hiu Man, Turski, Alice L., Venkat, Rohit, Waldman, Leah E., Wang, Kaidi, Wang, Tracy, Wei, Jeffrey W., Wu, Dennis Y., Xiong, David D., Yu, Jack, Zhou, Karen, McNeil, Gerard P., Fernandez, Robert W., Menzies, Patrick Gomez, Gu, Tingting, Buhler, Jeremy, Mardis, Elaine R., Elgin, Sarah C.R.
Publicado en G3 (Bethesda) (2017)