Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud
Griffith, Malachi, Walker, Jason R, Spies, Nicholas C, Ainscough, Benjamin J, Griffith, Obi L
Published in PLoS computational biology (01.08.2015)
Published in PLoS computational biology (01.08.2015)
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Journal Article
High-performance web services for querying gene and variant annotation
Xin, Jiwen, Mark, Adam, Afrasiabi, Cyrus, Tsueng, Ginger, Juchler, Moritz, Gopal, Nikhil, Stupp, Gregory S, Putman, Timothy E, Ainscough, Benjamin J, Griffith, Obi L, Torkamani, Ali, Whetzel, Patricia L, Mungall, Christopher J, Mooney, Sean D, Su, Andrew I, Wu, Chunlei
Published in Genome Biology (06.05.2016)
Published in Genome Biology (06.05.2016)
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Journal Article
DoCM: a database of curated mutations in cancer
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
Published in Nature methods (01.10.2016)
Published in Nature methods (01.10.2016)
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Genome-wide association study of CSF levels of 59 alzheimer's disease candidate proteins: significant associations with proteins involved in amyloid processing and inflammation
Kauwe, John S K, Bailey, Matthew H, Ridge, Perry G, Perry, Rachel, Wadsworth, Mark E, Hoyt, Kaitlyn L, Staley, Lyndsay A, Karch, Celeste M, Harari, Oscar, Cruchaga, Carlos, Ainscough, Benjamin J, Bales, Kelly, Pickering, Eve H, Bertelsen, Sarah, Fagan, Anne M, Holtzman, David M, Morris, John C, Goate, Alison M
Published in PLoS genetics (01.10.2014)
Published in PLoS genetics (01.10.2014)
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Journal Article
Phosphorylated Tau-Aβ42 Ratio as a Continuous Trait for Biomarker Discovery for Early-Stage Alzheimer’s Disease in Multiplex Immunoassay Panels of Cerebrospinal Fluid
Harari, Oscar, Cruchaga, Carlos, Kauwe, John S.K, Ainscough, Benjamin J, Bales, Kelly, Pickering, Eve H, Bertelsen, Sarah, Fagan, Anne M, Holtzman, David M, Morris, John C, Goate, Alison M
Published in Biological psychiatry (1969) (01.05.2014)
Published in Biological psychiatry (1969) (01.05.2014)
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Journal Article
DGIdb 2.0: mining clinically relevant drug-gene interactions
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
Published in Nucleic acids research (04.01.2016)
Published in Nucleic acids research (04.01.2016)
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Journal Article
Convergent loss of PTEN leads to clinical resistance to a PI(3)Kα inhibitor
Juric, Dejan, Castel, Pau, Griffith, Malachi, Griffith, Obi L., Won, Helen H., Ellis, Haley, Ebbesen, Saya H., Ainscough, Benjamin J., Ramu, Avinash, Iyer, Gopa, Shah, Ronak H., Huynh, Tiffany, Mino-Kenudson, Mari, Sgroi, Dennis, Isakoff, Steven, Thabet, Ashraf, Elamine, Leila, Solit, David B., Lowe, Scott W., Quadt, Cornelia, Peters, Malte, Derti, Adnan, Schegel, Robert, Huang, Alan, Mardis, Elaine R., Berger, Michael F., Baselga, José, Scaltriti, Maurizio
Published in Nature (London) (12.02.2015)
Published in Nature (London) (12.02.2015)
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Journal Article
CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer
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
Published in Nature genetics (01.02.2017)
Published in Nature genetics (01.02.2017)
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Journal Article
The prognostic effects of somatic mutations in ER-positive breast cancer
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.
Published in Nature communications (04.09.2018)
Published in Nature communications (04.09.2018)
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Journal Article
Organizing knowledge to enable personalization of medicine in cancer
Good, Benjamin M, Ainscough, Benjamin J, McMichael, Josh F, Su, Andrew I, Griffith, Obi L
Published in Genome biology (27.08.2014)
Published in Genome biology (27.08.2014)
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Journal Article
A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data
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.
Published in Nature genetics (01.12.2018)
Published in Nature genetics (01.12.2018)
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Journal Article
Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples
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.
Published in Genetics in medicine (01.04.2019)
Published in Genetics in medicine (01.04.2019)
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Journal Article
CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase
Krysiak, Kilannin, Danos, Arpad M, Saliba, Jason, McMichael, Joshua F, Coffman, Adam C, Kiwala, Susanna, Barnell, Erica K, Sheta, Lana, Grisdale, Cameron J, Kujan, Lynzey, Pema, Shahil, Lever, Jake, Ridd, Sarah, Spies, Nicholas C, Andric, Veronica, Chiorean, Andreea, Rieke, Damian T, Clark, Kaitlin A, Reisle, Caralyn, Venigalla, Ajay C, Evans, Mark, Jani, Payal, Takahashi, Hideaki, Suda, Avila, Horak, Peter, Ritter, Deborah I, Zhou, Xin, Ainscough, Benjamin J, Delong, Sean, Kesserwan, Chimene, Lamping, Mario, Shen, Haolin, Marr, Alex R, Hoang, My H, Singhal, Kartik, Khanfar, Mariam, Li, Brian V, Lin, Wan-Hsin, Terraf, Panieh, Corson, Laura B, Salama, Yasser, Campbell, Katie M, Farncombe, Kirsten M, Ji, Jianling, Zhao, Xiaonan, Xu, Xinjie, Kanagal-Shamanna, Rashmi, King, Ian, Cotto, Kelsy C, Skidmore, Zachary L, Walker, Jason R, Zhang, Jinghui, Milosavljevic, Aleksandar, Patel, Ronak Y, Giles, Rachel H, Kim, Raymond H, Schriml, Lynn M, Mardis, Elaine R, Jones, Steven J M, Raca, Gordana, Rao, Shruti, Madhavan, Subha, Wagner, Alex H, Griffith, Malachi, Griffith, Obi L
Published in Nucleic acids research (06.01.2023)
Published in Nucleic acids research (06.01.2023)
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Journal Article
Molecular phylogenetics of the burrowing crayfish genus Fallicambarus (Decapoda: Cambaridae)
Ainscough, Benjamin J., Breinholt, Jesse W., Robison, Henry W., Crandall, Keith A.
Published in Zoologica scripta (01.05.2013)
Published in Zoologica scripta (01.05.2013)
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Journal Article
Abstract 3289: Implementing evolving clinical standards in a variant interpretation knowledgebase
Krysiak, Kilannin, Danos, Arpad M., Wagner, Alex H., Kiwala, Susanna, McMichael, Joshua F., Coffman, Adam C., Barnell, Erica K., Feng, Yan-Yang, Ainscough, Benjamin J., Ramirez, Cody A., Griffith, Malachi, Griffith, Obi L.
Published in Cancer research (Chicago, Ill.) (01.07.2018)
Published in Cancer research (Chicago, Ill.) (01.07.2018)
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Journal Article
Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud: e1004393
Griffith, Malachi, Walker, Jason R, Spies, Nicholas C, Ainscough, Benjamin J, Griffith, Obi L
Published in PLoS computational biology (01.08.2015)
Published in PLoS computational biology (01.08.2015)
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Journal Article
Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia
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
Published in Experimental hematology (01.07.2016)
Published in Experimental hematology (01.07.2016)
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Journal Article
Abstract A2-42: Identifying clinically important somatic mutations through a knowledge-based approach
Ainscough, Benjamin J., Griffith, Malachi, Kunisaki, Jason, Coffman, Adam, McMichael, Joshua F., Eldred, James M., Walker, Jason R., Fulton, Robert S., Wilson, Richard K., Griffith, Obi L., Mardis, Elaine R.
Published in Cancer research (Chicago, Ill.) (15.11.2015)
Published in Cancer research (Chicago, Ill.) (15.11.2015)
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Journal Article
Abstract PR01: Identifying clinically important somatic mutations through a knowledge-based approach
Ainscough, Benjamin J., Griffith, Malachi, Kunisaki, Jason, Coffman, Adam, McMichael, Joshua F., Eldred, James M., Walker, Jason R., Fulton, Robert S., Wilson, Richard K., Griffith, Obi L., Mardis, Elaine R.
Published in Cancer research (Chicago, Ill.) (15.11.2015)
Published in Cancer research (Chicago, Ill.) (15.11.2015)
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Journal Article
Abstract A1-44: Clinical cancer sequencing and integrated analysis of whole genomes, exomes and transcriptomes
Griffith, Malachi, Griffith, Obi L., Ramu, Avinash, Ainscough, J Benjamin, Krysiak, Kilannin, Choudhary, Mayank, Skidmore, Zachary, Tan, Benjamin, Ramaswamy, Govindan, Tine, Brian Van, Ellis, Matthew J., Ley, Timothy J., Wilson, Richard K., Mardis, Elaine R.
Published in Cancer research (Chicago, Ill.) (15.11.2015)
Published in Cancer research (Chicago, Ill.) (15.11.2015)
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