GenVisR: Genomic Visualizations in R

por Skidmore, Zachary L., Wagner, Alex H., Lesurf, Robert, Campbell, Katie M., Kunisaki, Jason, Griffith, Obi L., Griffith, Malachi
Publicado en Bioinformatics (2016)

Prioritization of Retinal Disease Genes: An Integrative Approach

por Wagner, Alex H., Taylor, Kyle R., DeLuca, Adam P., Casavant, Thomas L., Mullins, Robert F., Stone, Edwin M., Scheetz, Todd E., Braun, Terry A.
Publicado en Hum Mutat (2013)

Optic nerve crush induces spatial and temporal gene expression patterns in retina and optic nerve of BALB/cJ mice

por Sharma, Tasneem P, McDowell, Colleen M, Liu, Yang, Wagner, Alex H, Thole, David, Faga, Benjamin P, Wordinger, Robert J, Braun, Terry A, Clark, Abbot F
Publicado 2014

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)

Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts

por Freshour, Sharon L, Kiwala, Susanna, Cotto, Kelsy C, Coffman, Adam C, McMichael, Joshua F, Song, Jonathan J, Griffith, Malachi, Griffith, Obi L, Wagner, Alex H
Publicado en Nucleic Acids Res (2020)

Whole-Gene Sequencing Investigation of SAT1 in Attempted Suicide

por Monson, Eric T., de Klerk, Kelly, Gaynor, Sophia C., Wagner, Alex H., Breen, Marie E., Parsons, Meredith, Casavant, Thomas L., Zandi, Peter P., Potash, James B., Willour, Virginia L.
Publicado en Am J Med Genet B Neuropsychiatr Genet (2016)

Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq

por Whitmore, S. Scott, Wagner, Alex H., DeLuca, Adam P., Drack, Arlene V., Stone, Edwin M., Tucker, Budd A., Zeng, Shemin, Braun, Terry A., Mullins, Robert F., Scheetz, Todd E.
Publicado en Exp Eye Res (2014)

DoCM: a database of curated mutations in cancer

por Ainscough, Benjamin J., Griffith, Malachi, Coffman, Adam C, Wagner, Alex H., Kunisaki, Jason, Choudhary, Mayank NK, McMichael, Joshua F., Fulton, Robert S., Wilson, Richard K., Griffith, Obi L., Mardis, Elaine R.
Publicado en Nat Methods (2016)

CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase

por Wagner, Alex H., Kiwala, Susanna, Coffman, Adam C., McMichael, Joshua F., Cotto, Kelsy C., Mooney, Thomas B., Barnell, Erica K., Krysiak, Kilannin, Danos, Arpad M., Walker, Jason, Griffith, Obi L., Griffith, Malachi
Publicado en JCO Clin Cancer Inform (2020)

Exon-level Expression Profiling of Ocular Tissues

por Wagner, Alex H., Anand, Nikhil, Wang, Wan-Heng, Chatterton, Jon E., Sun, Duo, Shepard, Allan, Jacobson, Nasreen, Pang, Iok-Hou, DeLuca, Adam, Casavant, Thomas L., Scheetz, Todd E., Mullins, Robert, Braun, Terry A., Clark, Abbot F.
Publicado 2013

A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data

por Ainscough, Benjamin J., Barnell, Erica K., Ronning, Peter, Campbell, Katie M., Wagner, Alex H., Fehniger, Todd A., Dunn, Gavin P., Uppaluri, Ravindra, Govindan, Ramaswamy, Rohan, Thomas E., Griffith, Malachi, Mardis, Elaine R., Swamidass, S. Joshua, Griffith, Obi L.
Publicado en Nat Genet (2018)

Collaborative, Multidisciplinary Evaluation of Cancer Variants Through Virtual Molecular Tumor Boards Informs Local Clinical Practices

por Rao, Shruti, Pitel, Beth, Wagner, Alex H., Boca, Simina M., McCoy, Matthew, King, Ian, Gupta, Samir, Park, Ben Ho, Warner, Jeremy L., Chen, James, Rogan, Peter K., Chakravarty, Debyani, Griffith, Malachi, Griffith, Obi L., Madhavan, Subha
Publicado en JCO Clin Cancer Inform (2020)

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)

Non-exomic and synonymous variants in ABCA4 are an important cause of Stargardt disease

por Braun, Terry A., Mullins, Robert F., Wagner, Alex H., Andorf, Jeaneen L., Johnston, Rebecca M., Bakall, Benjamin B., Deluca, Adam P., Fishman, Gerald A., Lam, Byron L., Weleber, Richard G., Cideciyan, Artur V., Jacobson, Samuel G., Sheffield, Val C., Tucker, Budd A., Stone, Edwin M.
Publicado 2013

Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards

por Danos, Arpad M., Ritter, Deborah I., Wagner, Alex H., Krysiak, Kilannin, Sonkin, Dmitriy, Micheel, Christine, McCoy, Matthew, Rao, Shruti, Raca, Gordana, Boca, Simina M., Roy, Angshumoy, Barnell, Erica K., McMichael, Joshua F., Kiwala, Susanna, Coffman, Adam C., Kujan, Lynzey, Kulkarni, Shashikant, Griffith, Malachi, Madhavan, Subha, Griffith, Obi L.
Publicado en Hum Mutat (2018)

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)

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)

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

por Wagner, Alex H., Walsh, Brian, Mayfield, Georgia, Tamborero, David, Sonkin, Dmitriy, Krysiak, Kilannin, Deu-Pons, Jordi, Duren, Ryan P., Gao, Jianjiong, McMurry, Julie, Patterson, Sara, del Vecchio Fitz, Catherine, Pitel, Beth A., Sezerman, Ozman U., Ellrott, Kyle, Warner, Jeremy L., Rieke, Damian T., Aittokallio, Tero, Cerami, Ethan, Ritter, Deborah I., Schriml, Lynn M., Freimuth, Robert R., Haendel, Melissa, Raca, Gordana, Madhavan, Subha, Baudis, Michael, Beckmann, Jacques S., Dienstmann, Rodrigo, Chakravarty, Debyani, Li, Xuan Shirley, Mockus, Susan, Elemento, Olivier, Schultz, Nikolaus, Lopez-Bigas, Nuria, Lawler, Mark, Goecks, Jeremy, Griffith, Malachi, Griffith, Obi L., Margolin, Adam A.
Publicado en Nat Genet (2020)

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)