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

od Griffith, Malachi, Walker, Jason R., Spies, Nicholas C., Ainscough, Benjamin J., Griffith, Obi L.
Wydane w PLoS Comput Biol (2015)

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

od 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
Wydane w Nucleic Acids Res (2018)

DGIdb 2.0: mining clinically relevant drug–gene interactions

od 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.
Wydane w 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

od 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.
Wydane w Clin Cancer Res (2015)

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

od 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.
Wydane w JCO Clin Cancer Inform (2019)

DGIdb - Mining the druggable genome

od 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.
Wydane 2013

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

od 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.
Wydane w Genet Med (2018)

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

od 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.
Wydane w 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

od 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.
Wydane w Clin Cancer Res (2017)

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

od 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.
Wydane w Nat Commun (2018)

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

od 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
Wydane w Nat Commun (2018)

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

od 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.
Wydane w Nat Commun (2018)

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

od 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.
Wydane w Exp Hematol (2016)

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

od 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.
Wydane w Clin Cancer Res (2020)

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

od 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
Wydane w Nat Genet (2017)

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

od 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.
Wydane w G3 (Bethesda) (2017)