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

di Griffith, Malachi, Walker, Jason R., Spies, Nicholas C., Ainscough, Benjamin J., Griffith, Obi L.
Pubblicato in PLoS Comput Biol (2015)

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

di 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
Pubblicato in Nucleic Acids Res (2018)

DGIdb 2.0: mining clinically relevant drug–gene interactions

di 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.
Pubblicato in 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

di 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.
Pubblicato in Clin Cancer Res (2015)

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

di 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.
Pubblicato in JCO Clin Cancer Inform (2019)

DGIdb - Mining the druggable genome

di 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.
Pubblicazione 2013

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

di 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.
Pubblicato in Genet Med (2018)

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

di 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.
Pubblicato in 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

di 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.
Pubblicato in Clin Cancer Res (2017)

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

di 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.
Pubblicato in Nat Commun (2018)

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

di 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
Pubblicato in Nat Commun (2018)

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

di 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.
Pubblicato in Nat Commun (2018)

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

di 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.
Pubblicato in Exp Hematol (2016)

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

di 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.
Pubblicato in Clin Cancer Res (2020)

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

di 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
Pubblicato in Nat Genet (2017)

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

di 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.
Pubblicato in G3 (Bethesda) (2017)