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  1. 1.   Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome
  2. Masood, Daniall; Ren, Luyao; Nguyen, Cu; Brundu, Francesco G; Zheng, Lily; Zhao,Yongmei; Jaeger, Erich; Li, Yong; Cha, Seong Won; Halpern, Aaron; Truong, Sean; Virata, Michael; Yan, Chunhua; Chen, Qingrong; Pang, Andy; Alberto, Reyes; Xiao, Chunlin; Yang, Zhaowei; Chen, Wanqiu; Wang, Charles; Cross, Frank; Catreux, Severine; Shi, Leming; Beaver, Julia A; Xiao, Wenming; Meerzaman, Daoud M
  3. Genome Biology. 2024, Jun 20; 25(1): 163.
  1. 2.   RrA, an enzyme from Rhodospirillum rubrum, is a prototype of a new family of short-chain L-asparaginases
  2. Zhang,Di; Czapinska, Honorata; Bochtler, Matthias; Wlodawer,Alexander; Lubkowski,Jacek
  3. Protein Science : a publication of the Protein Society. 2024, Apr; 33(4): e4920.
  1. 3.   Protocol for the saturation and multiplexing of genetic variants using CRISPR-Cas9
  2. Sahu,Sounak; Sullivan,Teresa; Southon,Eileen; Caylor,Dylan; Geh, Josephine; Sharan,Shyam
  3. STAR Protocols. 2023, Nov 08; 4(4): 102702.
  1. 4.   Protocol for using single-cell sequencing to study the heterogeneity of NF1 nerve sheath tumors from clinical biospecimens
  2. Zhang, Xiyuan; Gopalan, Vishaka; Syed,Neeraja; Hannenhalli, Sridhar; Shern, Jack F
  3. STAR Protocols. 2023, May 10; 4(2): 102297.
  1. 5.   Gene network landscape of mouse splenocytes reveals integrin complex as the A151 ODN-responsive hub molecule in the immune transcriptome
  2. Yazar, Volkan; Yilmaz, Ismail Cem; Bulbul, Artun; Klinman, Dennis M; Gursel, Ihsan
  3. Molecular Therapy. Nucleic Acids. 2023, Mar 14; 31: 553-565.
  1. 6.   IFN gamma Is a Key Link between Obesity and Th1-Mediated AutoImmune Diseases
  2. Bae,Heekyong; Choi, Myung-Sook; Kim, Suntae; Young,Howard; Gershwin, M. Eric; Jeon, Seon-Min; Kwon, Eun-Young
  3. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. 2021, Jan; 22(1):
  1. 7.   Novel targets identified by integrated cancer-stromal interactome analysis of pancreatic adenocarcinoma
  2. Hiroshima, Yukihiko; Kasajima, Rika; Kimura, Yayoi; Komura, Daisuke; Ishikawa, Shumpei; Ichikawa, Yasushi; Bouvet, Michael; Yamamoto, Naoto; Oshima, Takashi; Morinaga, Soichiro; Singh,Shree Ram; Hoffman, Robert M; Endo, Itaru; Miyagi, Yohei
  3. Cancer letters. 2020, Jan 28; 469: 217-227.
  1. 8.   SL-BioDP: Multi-Cancer Interactive Tool for Prediction of Synthetic Lethality and Response to Cancer Treatment
  2. Deng,Xiang; Das, Shaoli; Valdez,Kristin; Camphausen, Kevin; Shankavaram, Uma
  3. Cancers. 2019, Nov; 11(11): pii: E1682.
  1. 9.   Predicting the broadly neutralizing antibody susceptibility of the HIV reservoir
  2. Yu, Wen-Han; Su, David; Torabi, Julia; Fennessey,Christine; Shiakolas, Andrea; Lynch, Rebecca; Chun, Tae-Wook; Doria-Rose, Nicole; Alter, Galit; Seaman, Michael S; Keele,Brandon; Lauffenburger, Douglas A; Julg, Boris
  3. JCI insight. 2019, Sep 05; 4(17): pii: 130153.
  1. 10.   Viral coinfection analysis using a MinHash toolkit
  2. Dawson, Eric T; Wagner,Sarah; Roberson, David; Yeager,Meredith; Boland,Joseph; Garrison, Erik; Chanock, Stephen; Schiffman, Mark; Raine-Bennett, Tina; Lorey, Thomas; Castle, Phillip E; Mirabello, Lisa; Durbin, Richard
  3. BMC bioinformatics. 2019, Jul 12; 20(1): 389.
  1. 11.   Integrated analysis of competing endogenous RNA network revealing potential prognostic biomarkers of hepatocellular carcinoma
  2. Liao, Xiwen; Wang, Xiangkun; Huang, Ketuan; Han, Chuangye; Deng, Jianlong; Yu, Tingdong; Yang, Chengkun; Huang, Rui; Liu, Xiaoguang; Yu, Long; Zhu, Guangzhi; Su, Hao; Qin, Wei; Zeng, Xianmin; Han, Bowen; Han, Quanfa; Liu, Zhengqian; Zhou, Xin; Gong, Yizhen; Liu, Zhengtao; Huang, Jianly; Winkler,Cheryl; O'Brien, Stephen J.; Ye, Xinping; Peng, Tao
  3. JOURNAL OF CANCER. 2019, Jun 2; 10(14): 3267-3283.
  1. 12.   Computational Structural Biology: Successes, Future Directions, and Challenges
  2. Nussinov, Ruth; Tsai, Chung-Jung; Shehu, Amarda; Jang, Hyunbum
  3. Molecules (Basel, Switzerland). 2019, Feb 1; 24(3):
  1. 13.   Transmission, Evolution, and Endogenization: Lessons Learned from Recent Retroviral Invasions
  2. Greenwood, Alex D; Ishida, Yasuko; O'Brien, Sean; Roca, Alfred L; Eiden, Maribeth V
  3. Microbiology and molecular biology reviews : MMBR. 2018, Mar; 1092-2172:(1): pii: e00044-17.
  1. 14.   Structure of the cytoplasmic domain of Yersinia pestis YscD, an essential component of the type III secretion system
  2. Lountos, G. T.; Tropea, J. E.; Waugh, D. S.
  3. Acta Crystallographica Section D-Biological Crystallography. 2012, Mar; 68: 201-209.
  1. 15.   Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
  2. O'Boyle, N. M.; Guha, R.; Willighagen, E. L.; Adams, S. E.; Alvarsson, J.; Bradley, J. C.; Filippov, I. V.; Hanson, R. M.; Hanwell, M. D.; Hutchison, G. R.; James, C. A.; Jeliazkova, N.; Lang, A.; Langner, K. M.; Lonie, D. C.; Lowe, D. M.; Pansanel, J.; Pavlov, D.; Spjuth, O.; Steinbeck, C.; Tenderholt, A. L.; Theisen, K. J.; Murray-Rust, P.
  3. Journal of Cheminformatics. 2011, Oct; 3
  1. 16.   Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology
  2. Gonzalez-Nilo, F. G.-N. F.; Perez-Acle, T.; Guinez-Molinos, S.; Geraldo, D. A.; Sandoval, C.; Yevenes, A.; Santos, L. S.; Laurie, V. F.; Mendoza, H.; Cachau, R. E.
  3. Biological Research. 2011 44(1): 43-51.
  1. 17.   Quality Assessment of Microarray Data in a Multicenter Study
  2. Archer, K. J.; Mas, V. R.; O'Brien, T. R.; Pfeiffer, R.; Lum, N. L.; Fisher, R. A.
  3. Diagnostic Molecular Pathology. 2009 18(1): 34-43.
  1. 18.   bioDBnet: the biological database network
  2. Mudunuri, U.; Che, A.; Yi, M.; Stephens, R. M.
  3. Bioinformatics. 2009 25(4): 555-556.
  1. 19.   EMatch: Discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps
  2. Lasker, K.; Dror, O.; Shatsky, M.; Nussinov, R.; Wolfson, H. J.
  3. Ieee-Acm Transactions on Computational Biology and Bioinformatics. 2007, Jan-Mar; 4(1): 28-39.
  1. 20.   T7 lytic phage-displayed peptide libraries exhibit less sequence bias than M13 filamentous phage-displayed peptide libraries
  2. Krumpe, L. R. H.; Atkinson, A. J.; Smythers, G. W.; Kandel, A.; Schumacher, K. M.; McMahon, J. B.; Makowski, L.; Mori, T.
  3. Proteomics. 2006, Aug; 6(15): 4210-4222.
  1. 21.   Computational intelligence, bioinformatics and computational biology: A brief overview of methods, problems and perspectives
  2. Kasabov, N.; Sidorov, I. A.; Dimitrov, D. S.
  3. Journal of Computational and Theoretical Nanoscience. 2005, DEC; 2(4): 473-491.
  1. 22.   Low molecular weight proteomic information distinguishes metastatic from benign pheochromocytoma
  2. Brouwers, F. M.; Petricoin, E. F.; Ksinantova, L.; Breza, J.; Rajapakse, V.; Ross, S.; Johann, D.; Mannelli, M.; Shulkin, B. L.; Kvetnansky, R.; Eisenhofer, G.; Walther, M. M.; Hitt, B. A.; Conrads, T. P.; Veenstra, T. D.; Mannion, D. P.; Wall, M. R.; Wolfe, G. M.; Fusaro, V. A.; Liotta, L. A.; Pacak, K.
  3. Endocrine-Related Cancer. 2005, JUN; 12(2): 263-272.
  1. 23.   Discovery of protein substructures in EM maps
  2. Lasker, K.; Dror, O.; Nussinov, R.; Wolfson, H.
  3. Algorithms in bioinformatics. 2005; 3692 : 423-434.
  1. 24.   Integration of microsatellite characteristics in the MHC region: a literature and sequence based analysis
  2. Gourraud, P. A.; Mano, S.; Barnetche, T.; Carrington, M.; Inoko, H.; Cambon-Thomsen, A.
  3. Tissue Antigens. 2004, NOV; 64(5): 543-555.
  1. 25.   Insights into amyloid structural formation and assembly through computational approaches
  2. Zanuy, D.; Gunasekaran, K.; Ma, B. Y.; Tsai, H. H.; Tsai, C. J.; Nussinov, R.
  3. Amyloid-Journal of Protein Folding Disorders. 2004, SEP; 11(3): 143-161.
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