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  1. 1.   Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC)
  2. Horak, Peter; Griffith, Malachi; Danos, Arpad M; Pitel, Beth A; Madhavan, Subha; Liu, Xuelu; Chow, Cynthia; Williams, Heather; Carmody, Leigh; Barrow-Laing, Lisa; Rieke, Damian; Kreutzfeldt, Simon; Stenzinger, Albrecht; Tamborero, David; Benary, Manuela; Rajagopal, Padma Sheila; Ida, Cristiane M; Lesmana, Harry; Satgunaseelan, Laveniya; Merker, Jason D; Tolstorukov, Michael Y; Campregher, Paulo Vidal; Warner, Jeremy L; Rao, Shruti; Natesan, Maya; Shen, Haolin; Venstrom, Jeffrey; Roy, Somak; Tao, Kayoko; Kanagal-Shamanna, Rashmi; Xu, Xinjie; Ritter, Deborah I; Pagel, Kym; Krysiak, Kilannin; Dubuc, Adrian; Akkari, Yassmine M; Li, Xuan Shirley; Lee, Jennifer; King, Ian; Raca, Gordana; Wagner, Alex H; Li, Marylin M; Plon, Sharon E; Kulkarni, Shashikant; Griffith, Obi L; Chakravarty, Debyani; Sonkin, Dmitriy
  3. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 2022, Jan 28;
  1. 2.   Relation of Quantitative Histologic and Radiologic Breast Tissue Composition Metrics With Invasive Breast Cancer Risk
  2. Abubakar, Mustapha; Fan, Shaoqi; Bowles, Erin Aiello; Widemann, Lea; Duggan, Maire A.; Pfeiffer, Ruth M.; Falk, Roni T.; Lawrence,Scott; Richert-Boe, Kathryn; Glass, Andrew G.; Kimes, Teresa M.; Figueroa, Jonine D.; Rohan, Thomas E.; Gierach, Gretchen L.
  3. JNCI cancer spectrum. 2021, Jun; 5(3):
  1. 3.   A network-based deep learning methodology for stratification of tumor mutations
  2. Liu, Chuang; Han, Zhen; Zhang, Zi-Ke; Nussinov,Ruth; Cheng, Feixiong
  3. Bioinformatics. 2021, Jan 08; 37(1): 82-88.
  1. 4.   ReactionCode: format for reaction searching, analysis, classification, transform, and encoding/decoding
  2. Delannee,Victorien; Nicklaus,Marc
  3. Journal of cheminformatics. 2020, Dec 03; 12(1): 72.
  1. 5.   High throughput assessment of biomarkers in tissue microarrays using artificial intelligence: PTEN loss as a proof-of-principle in multi-center prostate cancer cohorts
  2. Harmon,Stephanie; Patel, Palak G; Sanford, Thomas H; Caven, Isabelle; Iseman, Rachael; Vidotto, Thiago; Picanço, Clarissa; Squire, Jeremy A; Masoudi, Samira; Mehralivand, Sherif; Choyke, Peter L; Berman, David M; Turkbey, Baris; Jamaspishvili, Tamara
  3. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc. 2020, Sep 03;
  1. 6.   The genomic and epigenomic evolutionary history of papillary renal cell carcinomas
  2. Zhu, Bin; Poeta, Maria Luana; Costantini, Manuela; Zhang, Tongwu; Shi, Jianxin; Sentinelli, Steno; Zhao, Wei; Pompeo, Vincenzo; Cardelli, Maurizio; Alexandrov, Boian S; Otlu, Burcak; Hua, Xing; Jones,Kristine; Brodie,Seth; Dabrowska, Malgorzata Ewa; Toro, Jorge R; Yeager,Meredith; Wang,Mingyi; Hicks,Belynda; Alexandrov, Ludmil B; Brown, Kevin M; Wedge, David C; Chanock, Stephen; Fazio, Vito Michele; Gallucci, Michele; Landi, Maria Teresa
  3. Nature communications. 2020, Jun 18; 11(1): 3096.
  1. 7.   Functional evaluation of five BRCA2 unclassified variants identified in a Sri Lankan cohort with inherited cancer syndromes using a mouse embryonic stem cell-based assay
  2. Sirisena, Nirmala; Biswas,Kajal; Sullivan,Teresa; Stauffer,Stacey; Cleveland, Linda; Southon,Eileen; Dissanayake, Vajira H W; Sharan,Shyam
  3. Breast cancer research : BCR. 2020, May 11; 22(1): 43.
  1. 8.   Cancer classification of single cell gene expression data by neural network
  2. Kim, Bong-Hyun; Yu, Kijin; Lee, Peter C W
  3. Bioinformatics (Oxford, England). 2020, MAR 1; 36(5): 1360-1366.
  1. 9.   Diversity and Complexity of the Large Surface Protein Family in the Compacted Genomes of Multiple Pneumocystis Species
  2. Ma, Liang; Chen, Zehua; Huang,Dawei; Cissé, Ousmane H; Rothenburger, Jamie L; Latinne, Alice; Bishop, Lisa; Blair, Robert; Brenchley, Jason M; Chabé, Magali; Deng, Xilong; Hirsch, Vanessa; Keesler, Rebekah; Kutty, Geetha; Liu, Yueqin; Margolis, Daniel; Morand, Serge; Pahar, Bapi; Peng, Li; Van Rompay, Koen K A; Song, Xiaohong; Song, Jun; Sukura, Antti; Thapar, Sabrina; Wang, Honghui; Weissenbacher-Lang, Christiane; Xu, Jie; Lee, Chao-Hung; Jardine, Claire; Lempicki, Richard A; Cushion, Melanie T; Cuomo, Christina A; Kovacs, Joseph A
  3. mBio. 2020, Mar-Apr; 11(2):
  1. 10.   Tumor Cell Biodiversity Drives Microenvironmental Reprogramming in Liver Cancer
  2. Ma, Lichun; Hernandez,Maria; Zhao,Yongmei; Mehta,Monika; Tran,Bao; Kelly,Michael; Rae,Zachary; Hernandez, Jonathan M; Davis, Jeremy L; Martin, Sean P; Kleiner, David E; Hewitt, Stephen M; Ylaya, Kris; Wood, Bradford J; Greten, Tim F; Wang, Xin Wei
  3. Cancer cell. 2019, Oct 14; 36(4): 418-430.
  1. 11.   Sphingolipid metabolism determines the therapeutic efficacy of nanoliposomal ceramide in acute myeloid leukemia
  2. Barth, Brian M; Wang, Weiyuan; Toran, Paul T; Fox, Todd E; Annageldiyev, Charyguly; Ondrasik, Regina M; Keasey, Nicole R; Brown, Timothy J; Devine, Viola G; Sullivan, Emily C; Cote, Andrea L; Papakotsi, Vasiliki; Tan, Su-Fern; Shanmugavelandy, Sriram S; Deering, Tye G; Needle, David B; Stern,Steve; Zhu, Junjia; Liao, Jason; Viny, Aaron D; Feith, David J; Levine, Ross L; Wang, Hong-Gang; Loughran, Thomas P; Sharma, Arati; Kester, Mark; Claxton, David F
  3. Blood advances. 2019, Sep 10; 3(17): 2598-2603.
  1. 12.   Prevalence of pathogenic/likely pathogenic variants in the 24 cancer genes of the ACMG Secondary Findings v2.0 list in a large cancer cohort and ethnicity-matched controls
  2. Kim, Jung; Luo, Wen; Wang, Mingyi; Wegman-Ostrosky, Talia; Frone, Megan N.; Johnston, Jennifer J.; Nickerson, Michael L.; Rotunno, Melissa; Li, Shengchao; Achatz, Maria I.; Brodie, Seth; Dean, Michael; de Andrade, Kelvin C.; Fortes, Fernanda P.; Gianferante, Matthew; Khincha, Payal; McMaster, Mary L.; McReynolds, Lisa J.; Pemov, Alexander; Pinheiro, Maisa; Santiago, Karina M.; Alter, Blanche P.; Caporaso, Neil E.; Gadalla, Shahinaz M.; Goldin, Lynn R.; Greene, Mark H.; Loud, Jennifer; Yang, Xiaohong R.; Freedman, Neal D.; Gapstur, Susan M.; Gaudet, Mia M.; Calista, Donato; Ghiorzo, Paola; Fargnoli, Maria Concetta; Nagore, Eduardo; Peris, Ketty; Puig, Susana; Landi, Maria Teresa; Hicks, Belynda; Zhu, Bin; Liu, Jia; Sampson, Joshua N.; Chanock, Stephen J.; Mirabello, Lisa J.; Morton, Lindsay M.; Biesecker, Leslie G.; Tucker, Margaret A.; Savage, Sharon A.; Goldstein, Alisa M.; Stewart, Douglas R.
  3. Genome medicine. 2018, Dec 24; 10(1):
  1. 13.   PROSTATEx Challenges for computerized classification of prostate lesions from multiparametric magnetic resonance images
  2. Armato, Samuel G; Huisman, Henkjan; Drukker, Karen; Hadjiiski, Lubomir; Kirby, Justin; Petrick, Nicholas; Redmond, George; Giger, Maryellen L; Cha, Kenny; Mamonov, Artem; Kalpathy-Cramer, Jayashree; Farahani, Keyvan
  3. Journal of medical imaging (Bellingham, Wash.). 2018, Oct; 5(4): 044501.
  1. 14.   How to Achieve Better Results Using PASS-Based Virtual Screening: Case Study for Kinase Inhibitors
  2. Pogodin, Pavel V; Lagunin, Alexey A; Rudik, Anastasia V; Filimonov, Dmitry A; Druzhilovskiy, Dmitry S; Nicklaus, Marc; Poroikov, Vladimir V
  3. Frontiers in chemistry. 2018, Apr 26; 6: 133.
  1. 15.   LUNGx Challenge for computerized lung nodule classification.
  2. Armato, Samuel G; Drukker, Karen; Li, Feng; Hadjiiski, Lubomir; Tourassi, Georgia D; Engelmann, Roger M; Giger, Maryellen L; Redmond, George; Farahani, Keyvan; Kirby, Justin S; Clarke, Laurence P
  3. Journal of medical imaging (Bellingham, Wash.). 2016, Oct; 3(4): 044506.
  1. 16.   The frequency of alpha(4)beta(7)(high) memory CD4(+) T cells correlates with susceptibility to rectal simian immunodeficiency virus infection
  2. Martinelli, E.; Veglia, F.; Goode, D.; Guerra-Perez, N.; Aravantinou, M.; Arthos, J.; Piatak, M., Jr.; Lifson, J. D.; Blanchard, J.; Gettie, A.; Robbiani, M.
  3. Journal of acquired immune deficiency syndromes (1999). 2013, 1-Dec; 64(4): 325-31.
  1. 17.   Correlating SHAPE signatures with three-dimensional RNA structures
  2. Bindewald, E.; Wendeler, M.; Legiewicz, M.; Bona, M. K.; Wang, Y.; Pritt, M. J.; Le Grice, S. F. J.; Shapiro, B. A.
  3. Rna-a Publication of the Rna Society. 2011, Sep; 17(9): 1688-1696.
  1. 18.   Molecular Architectures of Trimeric SIV and HIV-1 Envelope Glycoproteins on Intact Viruses: Strain-Dependent Variation in Quaternary Structure
  2. White, T. A.; Bartesaghi, A.; Borgnia, M. J.; Meyerson, J. R.; de la Cruz, M. J. V.; Bess, J. W.; Nandwani, R.; Hoxie, J. A.; Lifson, J. D.; Milne, J. L. S.; Subramaniam, S.
  3. Plos Pathogens. 2010, Dec; 6(12): 14.
  1. 19.   Tumor antigen analysis in neuroblastoma by serological interrogation of bioinformatic data
  2. Kohler, M. E.; Johnson, B. D.; Palen, K.; Chen, Q. R.; Khan, J.; Orentas, R. J.
  3. Cancer Science. 2010, Nov; 101(11): 2316-2324.
  1. 20.   The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
  2. Shi, L. M.; Campbell, G.; Jones, W. D.; Campagne, F.; Wen, Z. N.; Walker, S. J.; Su, Z. Q.; Chu, T. M.; Goodsaid, F. M.; Pusztai, L.; Shaughnessy, J. D.; Oberthuer, A.; Thomas, R. S.; Paules, R. S.; Fielden, M.; Barlogie, B.; Chen, W. J.; Du, P.; Fischer, M.; Furlanello, C.; Gallas, B. D.; Ge, X. J.; Megherbi, D. B.; Symmans, W. F.; Wang, M. D.; Zhang, J.; Bitter, H.; Brors, B.; Bushel, P. R.; Bylesjo, M.; Chen, M. J.; Cheng, J.; Chou, J.; Davison, T. S.; Delorenzi, M.; Deng, Y. P.; Devanarayan, V.; Dix, D. J.; Dopazo, J.; Dorff, K. C.; Elloumi, F.; Fan, J. Q.; Fan, S. C.; Fan, X. H.; Fang, H.; Gonzaludo, N.; Hess, K. R.; Hong, H. X.; Huan, J.; Irizarry, R. A.; Judson, R.; Juraeva, D.; Lababidi, S.; Lambert, C. G.; Li, L.; Li, Y. N.; Li, Z.; Lin, S. M.; Liu, G. Z.; Lobenhofer, E. K.; Luo, J.; Luo, W.; McCall, M. N.; Nikolsky, Y.; Pennello, G. A.; Perkins, R. G.; Philip, R.; Popovici, V.; Price, N. D.; Qian, F.; Scherer, A.; Shi, T. L.; Shi, W. W.; Sung, J.; Thierry-Mieg, D.; Thierry-Mieg, J.; Thodima, V.; Trygg, J.; Vishnuvajjala, L.; Wang, S. J.; Wu, J. P.; Wu, Y. C.; Xie, Q. A.; Yousef, W. A.; Zhang, L. A.; Zhang, X. G.; Zhong, S.; Zhou, Y. M.; Zhu, S.; Arasappan, D.; Bao, W. J.; Lucas, A. B.; Berthold, F.; Brennan, R. J.; Buness, A.; Catalano, J. G.; Chang, C.; Chen, R.; Cheng, Y. Y.; Cui, J. A.; Czika, W.; Demichelis, F.; Deng, X. T.; Dosymbekov, D.; Eils, R.; Feng, Y.; Fostel, J.; Fulmer-Smentek, S.; Fuscoe, J. C.; Gatto, L.; Ge, W. G.; Goldstein, D. R.; Guo, L.; Halbert, D. N.; Han, J.; Harris, S. C.; Hatzis, C.; Herman, D.; Huang, J. P.; Jensen, R. V.; Jiang, R.; Johnson, C. D.; Jurman, G.; Kahlert, Y.; Khuder, S. A.; Kohl, M.; Li, J. Y.; Li, M. L.; Li, Q. Z.; Li, S.; Li, Z. G.; Liu, J.; Liu, Y.; Liu, Z. C.; Meng, L.; Madera, M.; Martinez-Murillo, F.; Medina, I.; Meehan, J.; Miclaus, K.; Moffitt, R. A.; Montaner, D.; Mukherjee, P.; Mulligan, G. J.; Neville, P.; Nikolskaya, T.; Ning, B. T.; Page, G. P.; Parker, J.; Parry, R. M.; Peng, X. J.; Peterson, R. L.; Phan, J. H.; Quanz, B.; Ren, Y.; Riccadonna, S.; Roter, A. H.; Samuelson, F. W.; Schumacher, M. M.; Shambaugh, J. D.; Shi, Q. A.; Shippy, R.; Si, S. Z.; Smalter, A.; Sotiriou, C.; Soukup, M.; Staedtler, F.; Steiner, G.; Stokes, T. H.; Sun, Q. L.; Tan, P. Y.; Tang, R.; Tezak, Z.; Thorn, B.; Tsyganova, M.; Turpaz, Y.; Vega, S. C.; Visintainer, R.; von Frese, J.; Wang, C.; Wang, E.; Wang, J. W.; Wang, W.; Westermann, F.; Willey, J. C.; Woods, M.; Wu, S. J.; Xiao, N. Q.; Xu, J.; Xu, L.; Yang, L.; Zeng, X. A.; Zhang, J. L.; Zhang, L.; Zhang, M.; Zhao, C.; Puri, R. K.; Scherf, U.; Tong, W. D.; Wolfinger, R. D.; Consortium, M.
  3. Pharmacogenomics Journal. 2010, Oct; S5-S16.
  1. 21.   Structure of the N-terminal fragment of Escherichia coli Lon protease
  2. Li, M.; Gustchina, A.; Rasulova, F. S.; Melnikov, E. E.; Maurizi, M. R.; Rotanova, T. V.; Dauter, Z.; Wlodawer, A.
  3. Acta Crystallographica Section D-Biological Crystallography. 2010, Aug; 66: 865-873.
  1. 22.   Identifying and characterizing recently transmitted viruses
  2. Keele, B. F.
  3. Current opinion in HIV and AIDS. 2010, Jul; 5(4): 327-34.
  1. 23.   RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapy
  2. Shao, W.; Kearney, M.; Maldarelli, F.; Mellors, J. W.; Stephens, R. M.; Lifson, J. D.; KewalRamani, V. N.; Ambrose, Z.; Coffin, J. M.; Palmer, S. E.
  3. Retrovirology. 2009 6: 101.
  1. 24.   Functional Redundancy of Exon 12 of BRCA2 Revealed by a Comprehensive Analysis of the c.6853A > G (p.I2285V) Variant
  2. Li, L. L.; Biswas, K.; Habib, L. A.; Kuznetsov, S. G.; Hamel, N.; Kirchhoff, T.; Wong, N.; Armel, S.; Chong, G.; Narod, S. A.; Claes, K.; Offit, K.; Robson, M. E.; Stauffer, S.; Sharan, S. K.; Foulkes, W. D.
  3. Human Mutation. 2009 30(11): 1543-1550.
  1. 25.   RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases
  2. Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J.
  3. Nucleic Acids Research. 2009 37(Database issue): D369-D373.
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