Opportunities and obstacles for deep learning in biology and medicine
Ching, Travers, Himmelstein, Daniel S., Beaulieu-Jones, Brett K., Kalinin, Alexandr A., Do, Brian T., Way, Gregory P., Ferrero, Enrico, Agapow, Paul-Michael, Zietz, Michael, Hoffman, Michael M., Xie, Wei, Rosen, Gail L., Lengerich, Benjamin J., Israeli, Johnny, Lanchantin, Jack, Woloszynek, Stephen, Carpenter, Anne E., Shrikumar, Avanti, Xu, Jinbo, Cofer, Evan M., Lavender, Christopher A., Turaga, Srinivas C., Alexandari, Amr M., Lu, Zhiyong, Harris, David J., DeCaprio, Dave, Qi, Yanjun, Kundaje, Anshul, Peng, Yifan, Wiley, Laura K., Segler, Marwin H. S., Boca, Simina M., Swamidass, S. Joshua, Huang, Austin, Gitter, Anthony, Greene, Casey S.
Published in Journal of the Royal Society interface (01.04.2018)
Published in Journal of the Royal Society interface (01.04.2018)
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Proteogenomic and metabolomic characterization of human glioblastoma
Gritsenko, Marina A., Kyle, Jennifer E., Cao, Song, Rykunov, Dmitry, Cornwell, MacIntosh, Petralia, Francesca, Wu, Yige, Reva, Boris, Kawaler, Emily, Olsen, Lindsey K., Liang, Wen-Wei, Wendl, Michael C., Caravan, Wagma, Ji, Jiayi, Petyuk, Vladislav A., Moon, Jamie, Moore, Ronald J., Krek, Azra, Zhu, Houxiang, McMichael, Joshua F., Lu, Shuangjia, Baral, Jessika, Yao, Lijun, Zink, Erika, Bloodsworth, Kent J., Satpathy, Shankha, Boca, Simina M., Chen, Feng, Ketchum, Karen A., Boja, Emily S., Hiltke, Tara, Mani, D.R., Chen, Xi S., Li, Qing Kay, Kim, Albert H., Fenyö, David, Mesri, Mehdi, Resnick, Adam C., Wang, Pei, Chheda, Milan G., Barnholtz-Sloan, Jill S., Rodland, Karin D., Liu, Tao, Ding, Li, Bauer, Thomas, Borucki, Melissa, Burke, Meghan C., Cai, Shuang, Calinawan, Anna P., Carr, Steven A., Chan, Daniel W., Charamut, Alyssa, Chesla, David, Chowdhury, Shrabanti, Cieślik, Marcin P., Culpepper, Houston, Demir, Emek, Dhir, Rajiv, Duffy, Elizabeth, Edwards, Robert, Gabriel, Stacey, Gabrovski, Nikolay, Garofano, Luciano, Gillette, Michael A., Hannick, Linda I., Hindenach, Barbara, Hoadley, Katherine A., Hostetter, Galen, Huang, Chen, Jaehnig, Eric, Ji, Nan, Jones, Corbin D., Kaspera, Wojciech, Lei, Jonathan, Li, Kai, Liu, Hongwei, Lubínski, Jan, Malc, Ewa, Malovannaya, Anna, McGarvey, Peter B., McGee, John, Mieczkowski, Piotr, Modugno, Francesmary, Ozbek, Umut, Paulovich, Amanda G., Piehowski, Paul D., Polonskaya, Larisa, Pruetz, Barbara, Ramkissoon, Shakti, Riggins, Gregory, Stawicki, Jakub, Tabor, Dave, Tansil, Darlene, Traer, Elie, Vatanian, Negin, Webster, Alex, Wen, Bo, Whiteaker, Jeffrey R., Zhang, Liwei, Zhao, Grace
Published in Cancer cell (12.04.2021)
Published in Cancer cell (12.04.2021)
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Journal Article
FWER and FDR control when testing multiple mediators
Sampson, Joshua N, Boca, Simina M, Moore, Steven C, Heller, Ruth
Published in Bioinformatics (15.07.2018)
Published in Bioinformatics (15.07.2018)
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Journal Article
On the heterozygosity of an admixed population
Boca, Simina M., Huang, Lucy, Rosenberg, Noah A.
Published in Journal of mathematical biology (01.12.2020)
Published in Journal of mathematical biology (01.12.2020)
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Journal Article
Npas1 + -Nkx2.1 + Neurons Are an Integral Part of the Cortico-pallido-cortical Loop
Abecassis, Zachary A, Berceau, Brianna L, Win, Phyo H, García, Daniela, Xenias, Harry S, Cui, Qiaoling, Pamukcu, Arin, Cherian, Suraj, Hernández, Vivian M, Chon, Uree, Lim, Byung Kook, Kim, Yongsoo, Justice, Nicholas J, Awatramani, Raj, Hooks, Bryan M, Gerfen, Charles R, Boca, Simina M, Chan, C Savio
Published in The Journal of neuroscience (22.01.2020)
Published in The Journal of neuroscience (22.01.2020)
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Journal Article
Genomic Landscapes of Human Breast and Colorectal Cancers
Wood, Laura D, Parsons, D. Williams, Jones, Siân, Lin, Jimmy, Sjöblom, Tobias, Leary, Rebecca J, Shen, Dong, Boca, Simina M, Barber, Thomas, Ptak, Janine, Silliman, Natalie, Szabo, Steve, Dezso, Zoltan, Ustyanksky, Vadim, Nikolskaya, Tatiana, Nikolsky, Yuri, Karchin, Rachel, Wilson, Paul A, Kaminker, Joshua S, Zhang, Zemin, Croshaw, Randal, Willis, Joseph, Dawson, Dawn, Shipitsin, Michail, Willson, James K.V, Sukumar, Saraswati, Polyak, Kornelia, Park, Ben Ho, Pethiyagoda, Charit L, Pant, P.V. Krishna, Ballinger, Dennis G, Sparks, Andrew B, Hartigan, James, Smith, Douglas R, Suh, Erick, Papadopoulos, Nickolas, Buckhaults, Phillip, Markowitz, Sanford D, Parmigiani, Giovanni, Kinzler, Kenneth W, Velculescu, Victor E, Vogelstein, Bert
Published in Science (American Association for the Advancement of Science) (16.11.2007)
Published in Science (American Association for the Advancement of Science) (16.11.2007)
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Journal Article
Group testing in mediation analysis
Derkach, Andriy, Moore, Steven C., Boca, Simina M., Sampson, Joshua N.
Published in Statistics in medicine (15.08.2020)
Published in Statistics in medicine (15.08.2020)
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Journal Article
Dissociable Roles of Pallidal Neuron Subtypes in Regulating Motor Patterns
Cui, Qiaoling, Pamukcu, Arin, Cherian, Suraj, Chang, Isaac Y M, Berceau, Brianna L, Xenias, Harry S, Higgs, Matthew H, Rajamanickam, Shivakumar, Chen, Yi, Du, Xixun, Zhang, Yu, McMorrow, Hayley, Abecassis, Zachary A, Boca, Simina M, Justice, Nicholas J, Wilson, Charles J, Chan, C Savio
Published in The Journal of neuroscience (05.05.2021)
Published in The Journal of neuroscience (05.05.2021)
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Journal Article
Serum biomarkers of habitual coffee consumption may provide insight into the mechanism underlying the association between coffee consumption and colorectal cancer
Guertin, Kristin A, Loftfield, Erikka, Boca, Simina M, Sampson, Joshua N, Moore, Steven C, Xiao, Qian, Huang, Wen-Yi, Xiong, Xiaoqin, Freedman, Neal D, Cross, Amanda J, Sinha, Rashmi
Published in The American journal of clinical nutrition (01.05.2015)
Published in The American journal of clinical nutrition (01.05.2015)
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Journal Article
Discovery of potential urine-accessible metabolite biomarkers associated with muscle disease and corticosteroid response in the mdx mouse model for Duchenne
Thangarajh, Mathula, Zhang, Aiping, Gill, Kirandeep, Ressom, Habtom W, Li, Zhenzhi, Varghese, Rency S, Hoffman, Eric P, Nagaraju, Kanneboyina, Hathout, Yetrib, Boca, Simina M
Published in PloS one (16.07.2019)
Published in PloS one (16.07.2019)
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Journal Article
Testing multiple biological mediators simultaneously
Boca, Simina M, Sinha, Rashmi, Cross, Amanda J, Moore, Steven C, Sampson, Joshua N
Published in Bioinformatics (15.01.2014)
Published in Bioinformatics (15.01.2014)
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Journal Article
Metabolomics in Epidemiology: Sources of Variability in Metabolite Measurements and Implications
SAMPSON, Joshua N, BOCA, Simina M, DA KE LIU, GONG YANG, YONG BING XIANG, WEI ZHENG, SINHA, Rashmi, CROSS, Amanda J, MOORE, Steven C, XIAO OU SHU, STOLZENBERG-SOLOMON, Rachael Z, MATTHEWS, Charles E, HSING, Ann W, YU TING TAN, JI, Bu-Tian, CHOW, Wong-Ho, CAR, Qiuyin
Published in Cancer epidemiology, biomarkers & prevention (01.04.2013)
Published in Cancer epidemiology, biomarkers & prevention (01.04.2013)
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Journal Article
Discovery of Metabolic Biomarkers for Duchenne Muscular Dystrophy within a Natural History Study
Boca, Simina M, Nishida, Maki, Harris, Michael, Rao, Shruti, Cheema, Amrita K, Gill, Kirandeep, Seol, Haeri, Morgenroth, Lauren P, Henricson, Erik, McDonald, Craig, Mah, Jean K, Clemens, Paula R, Hoffman, Eric P, Hathout, Yetrib, Madhavan, Subha
Published in PloS one (15.04.2016)
Published in PloS one (15.04.2016)
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Journal Article
Patient-oriented gene set analysis for cancer mutation data
Boca, Simina M, Kinzler, Kenneth W, Velculescu, Victor E, Vogelstein, Bert, Parmigiani, Giovanni
Published in Genome biology (01.01.2010)
Published in Genome biology (01.01.2010)
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Journal Article
Sources of variability in metabolite measurements from urinary samples
Xiao, Qian, Moore, Steven C, Boca, Simina M, Matthews, Charles E, Rothman, Nathaniel, Stolzenberg-Solomon, Rachael Z, Sinha, Rashmi, Cross, Amanda J, Sampson, Joshua N
Published in PloS one (01.05.2014)
Published in PloS one (01.05.2014)
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Journal Article
A prospective study of serum metabolites and colorectal cancer risk
Cross, Amanda J., Moore, Steven C., Boca, Simina, Huang, Wen‐Yi, Xiong, Xiaoqin, Stolzenberg‐Solomon, Rachael, Sinha, Rashmi, Sampson, Joshua N.
Published in Cancer (01.10.2014)
Published in Cancer (01.10.2014)
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Journal Article
Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
Wang, Zhaoming, Diver, W Ryan, Dorronsoro, Miren, Dossus, Laure, Gago-Dominguez, Manuela, Mirabello, Lisa, Gaudet, Mia M, Giffen, Carol, Giles, Graham G, Goggins, Michael, Savage, Sharon A, Gorlick, Richard, Guo, Huan, He, Qincheng, Helzlsouer, Kathy, Henderson, Brian, Hjalgrim, Henrik, Hoover, Robert N, Hu, Zhibin, Huang, Ming-Shyan, Jacobs, Eric J, Jeon, Hyo-Sung, Jin, Li, Kaaks, Rudolph, Rajaraman, Preetha, Kane, Eleanor, Karagas, Margaret R, Kim, Hee Nam, Kim, Jun Suk, Kurtz, Robert C, Kweon, Sun-Seog, Lawrence, Charles, Albanes, Demetrius, Li, Haixin, Li, Jihua, Li, Yao-Jen, Li, Yuqing, Lindstrom, Sara, Liu, Chenwei, Liu, Jianjun, Lloreta, Josep, An, She-Juan, Lund, Eiluv, Malats, Nuria, Mannisto, Satu, Le Marchand, Loic, Marina, Neyssa, Andersson, Ulrika, Melbye, Mads, Monnereau, Alain, Montalvan, Rebecca, Moore, Lee E, Andriole, Gerald, North, Kari E, Pao, William, Andrulis, Irene L, Patiño-Garcia, Ana, Peeters, Petra H M, Prokunina-Olsson, Ludmila, Riboli, Elio, Riby, Jacques, Arici, Cecilia, Sesso, Howard D, Shen, Hongbing, Armstrong, Bruce K, Shiraishi, Kouya, Skibola, Christine F, Sung, Jae Sook, Austin, Melissa A, Thompson, Carrie A, Vajdic, Claire M, Villano, Danylo J, Wang, Chih-Liang, Wang, Jiu-Cun, Wei, Fusheng, Weiderpass, Elisabete, Weinstein, Stephanie, Wolpin, Brian M, Wu, Tangchun, Yoon, Ho-Il, Yu, Chong-Jen, Yu, Kai, Zhang, Xu-Chao, Zhao, Zhenhong, Berg, Christine, Ferri, Giovanni M, Hartge, Patricia, Hsiung, Chao Agnes, VanDenBerg, David, Slager, Susan L, Chanock, Stephen J, Bueno-de-Mesquita, H Bas, Carta, Angela, Chang, I-Shou, Chen, Chung-Hsing, Chen, Ying-Hsiang, Choi, Jin Eun, Conti, David, Cozen, Wendy, Crous-Bou, Marta
Published in JNCI : Journal of the National Cancer Institute (01.12.2015)
Published in JNCI : Journal of the National Cancer Institute (01.12.2015)
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Journal Article
Human metabolic correlates of body mass index
Moore, Steven C., Matthews, Charles E., Sampson, Joshua N., Stolzenberg-Solomon, Rachael Z., Zheng, Wei, Cai, Qiuyin, Tan, Yu Ting, Chow, Wong-Ho, Ji, Bu-Tian, Liu, Da Ke, Xiao, Qian, Boca, Simina M., Leitzmann, Michael F., Yang, Gong, Xiang, Yong Bing, Sinha, Rashmi, Shu, Xiao Ou, Cross, Amanda J.
Published in Metabolomics (01.04.2014)
Published in Metabolomics (01.04.2014)
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