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  1. 1.   Inferring phase transitions and critical exponents from limited observations with thermodynamic maps
  2. Herron, Lukas; Mondal, Kinjal; Schneekloth,Jay; Tiwary, Pratyush
  3. Proceedings of the National Academy of Sciences of the United States of America. 2024, Dec 24; 121(52): e2321971121.
  1. 2.   Proteogenomic characterization of pancreatic ductal adenocarcinoma
  2. Cao, Liwei; Huang, Chen; Zhou, Daniel Cui; Hu, Yingwei; Lih, T. Mamie; Savage, Sara R.; Krug, Karsten; Clark, David J.; Schnaubelt, Michael; Chen, Lijun; Leprevost, Felipe da Veiga; Eguez, Rodrigo Vargas; Yang, Weiming; Pan, Jianbo; Wen, Bo; Dou, Yongchao; Jiang, Wen; Liao, Yuxing; Shi, Zhiao; Terekhanova, Nadezhda; Cao, Song; Lu, Rita Jui-Hsien; Li, Yize; Liu, Ruiyang; Zhu, Houxiang; Ronning, Peter; Wu, Yige; Wyczalkowski, Matthew A.; Easwaran, Hariharan; Danilova, Ludmila; Mer, Arvind Singh; Yoo, Seungyeul; Wang, Joshua M.; Liu, Wenke; Haibe-Kains, Benjamin; Thiagarajan,Mathangi; Jewell, Scott D.; Hostetter, Galen; Newton, Chelsea J.; Li, Qing Kay; Roehr, Michael H.; Fenyo, David; Wang, Pei; Nesvizhskii, Alexey; Mani, D. R.; Omenn, Gilbert S.; Boja, Emily S.; Mesri, Mehdi; Robles, Ana; Rodriguez, Henry; Bathe, Oliver F.; Chan, Daniel W.; Hruban, Ralph H.; Ding, Li; Zhang, Bing; Zhang, Hui
  3. Cell. 2021, Sep 16; 184(19): 5031-5052.e26.
  1. 3.   Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma
  2. Huang, Chen; Chen, Lijun; Savage, Sara R.; Eguez, Rodrigo Vargas; Dou, Yongchao; Li, Yize; Leprevost, Felipe da Veiga; Jaehnig, Eric J.; Lei, Jonathan T.; Wen, Bo; Schnaubelt, Michael; Krug, Karsten; Song, Xiaoyu; Cieslik, Marcin; Chang, Hui-Yin; Wyczalkowski, Matthew A.; Li, Kai; Colaprico, Antonio; Li, Qing Kay; Clark, David J.; Hu, Yingwei; Cao, Liwei; Pan, Jianbo; Wang, Yuefan; Cho, Kyung-Cho; Shi, Zhiao; Liao, Yuxing; Jiang, Wen; Anurag, Meenakshi; Ji, Jiayi; Yoo, Seungyeul; Zhou, Daniel Cui; Liang, Wen-Wei; Wendl, Michael; Vats, Pankaj; Carr, Steven A.; Mani, D. R.; Zhang, Zhen; Qian, Jiang; Chen, Xi S.; Pico, Alexander R.; Wang, Pei; Chinnaiyan, Arul M.; Ketchum, Karen A.; Kinsinger, Christopher R.; Robles, Ana; An, Eunkyung; Hiltke, Tara; Mesri, Mehdi; Thiagarajan,Mathangi; Weaver, Alissa M.; Sikora, Andrew G.; Lubinski, Jan; Wierzbicka, Malgorzata; Wiznerowicz, Maciej; Satpathy, Shankha; Gillette, Michael A.; Miles, George; Ellis, Matthew J.; Omenn, Gilbert S.; Rodriguez, Henry; Boja, Emily S.; Dhanasekaran, Saravana M.; Ding, Li; Nesvizhskii, Alexey; El-Naggar, Adel K.; Chan, Daniel W.; Zhang, Hui; Zhang, Bing
  3. Cancer Cell. 2021, Mar 8; 39(3): 361-379.
  1. 4.   Deep Proteomics Using Two Dimensional Data Independent Acquisition Mass Spectrometry
  2. Cho, Kyung-Cho; Clark, David J.; Schnaubelt, Michael; Teo, Guo Ci; Leprevost, Felipe Veiga; Bocik,William; Boja, Emily S.; Hiltke, Tara; Nesvizhskii, Alexey; Zhang, Hui
  3. ANALYTICAL CHEMISTRY. 2020, Mar 17; 92(6): 4217-4225.
  1. 5.   Examination of disease-based selection, demographic history and population structure in European Y-chromosome haplogroup I
  2. Sezgin, E.; Drosdak, A.; McIntosh, C.; Kessing, B.; Lautenberger, J. A.; Goedert, J. J.; Phair, J. P.; Troyer, J. L.; Smith, M. W.; O'Brien, S. J.
  3. Journal of Human Genetics. 2010, Sep; 55(9): 613-620.
  1. 6.   Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line
  2. Vogel, C.; Abreu, R. D.; Ko, D. J.; Le, S. Y.; Shapiro, B. A.; Burns, S. C.; Sandhu, D.; Boutz, D. R.; Marcotte, E. M.; Penalva, L. O.
  3. Molecular Systems Biology. 2010, Aug; 6: 9.
  1. 7.   Genomic Analyses of Musashi1 Downstream Targets Show a Strong Association with Cancer-related Processes
  2. Abreu, R. D.; Sanchez-Diaz, P. C.; Vogel, C.; Burns, S. C.; Ko, D. J.; Burton, T. L.; Vo, D. T.; Chennasamudaram, S.; Le, S. Y.; Shapiro, B. A.; Penalva, L.
  3. Journal of Biological Chemistry. 2009 284(18): 12125-12135.
  1. 8.   Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
  2. Huang, D. W.; Sherman, B. T.; Lempicki, R. A.
  3. Nucleic Acids Research. 2009 37(1): 1-13.
  1. 9.   The Evolutionary Dynamics of the Lion Panthera leo Revealed by Host and Viral Population Genomics
  2. Antunes, A.; Troyer, J. L.; Roelke, M. E.; Pecon-Slattery, J.; Packer, C.; Winterbach, C.; Winterbach, H.; Hemson, G.; Frank, L.; Stander, P.; Siefert, L.; Driciru, M.; Funston, P. J.; Alexander, K. A.; Prager, K. C.; Mills, G.; Wildt, D.; Bush, M.
  3. Plos Genetics. 2008 4(11):
  1. 10.   Phylogeography and population history of the crab-eating fox (Cerdocyon thous)
  2. Tchaicka, L.; Eizirik, E.; De Oliveira, T. G.; Candido, J. F.; Freitas, T. R. O.
  3. Molecular Ecology. 2007, Feb; 16(4): 819-838.
  1. 11.   Transcriptomic analysis of an in vitro murine model of ovarian carcinoma: Functional similarity to the human disease and identification of prospective tumoral markers and targets
  2. Urzua, U.; Roby, K. F.; Gangi, L. M.; Cherry, J. M.; Powell, J. I.; Munroe, D. J.
  3. Journal of Cellular Physiology. 2006, MAR; 206(3): 594-602.
  1. 12.   Comprehensive analysis of pathway or functionally related gene expression in the National Cancer Institute's anticancer screen
  2. Huang, R.; Wallqvist, A.; Covell, D. G.
  3. Genomics. 2006, MAR; 87(3): 315-328.
  1. 13.   Preconceptional fasting of fathers alters serum glucose in offspring of mice
  2. Anderson, L. M.; Riffle, L.; Wilson, R.; Travlos, G. S.; Lubomirski, M. S.; Alvord, W. G.
  3. Nutrition. 2006, MAR; 22(3): 327-331.
  1. 14.   Therapeutic modulation of Akt activity and antitumor efficacy of interleukin-12 against orthotopic murine neuroblastoma
  2. Khan, T.; Hixon, J. A.; Stauffer, J. K.; Lincoln, E.; Back, T. C.; Brenner, J.; Lockett, S.; Nagashima, K.; Powell, D.; Wigginton, J. M.
  3. Journal of the National Cancer Institute. 2006, FEB 1; 98(3): 190-202.
  1. 15.   LC-MS in metabonomics: Optimization of experimental conditions for the analysis of metabolites in human urine
  2. Waybright, T. J.; Van, Q. N.; Muschik, G. M.; Conrads, T. P.; Veenstra, T. D.; Issaq, H. J.
  3. Journal of Liquid Chromatography & Related Technologies. 2006 29(17): 2475-2497.
  1. 16.   Genetic variation, nucleotide diversity, and linkage disequilibrium in seven telomere stability genes suggest that these genes may be under constraint
  2. Savage, S. A.; Stewart, B. J.; Eckert, A.; Kiley, M.; Liao, J. S.; Chanock, S. J.
  3. Human Mutation. 2005, OCT; 26(4): 343-350.
  1. 17.   Formylpeptide receptor FPR and the rapid growth of malignant human gliomas
  2. Zhou, Y.; Bian, X. W.; Le, Y. Y.; Gong, W. H.; Hu, J. Y.; Zhang, X.; Wang, L. H.; Iribarren, P.; Salcedo, R.; Howard, O. M. Z.; Farrar, W.; Wang, J. M.
  3. Journal of the National Cancer Institute. 2005, JUN 1; 97(11): 823-835.
  1. 18.   Medroxyprogesterone acetate elevation of Nm23-H1 metastasis suppressor expression in hormone receptor-negative breast cancer
  2. Palmieri, D.; Halverson, D. O.; Ouatas, T.; Horak, C. E.; Salerno, M.; Johnson, J.; Figg, W. D.; Hollingshead, M.; Hursting, S.; Berrigan, D.; Steinberg, S. M.; Merino, M. J.; Steeg, P. S.
  3. Journal of the National Cancer Institute. 2005, MAY 4; 97(9): 632-642.
  1. 19.   Weak palindromic consensus sequences are a common feature found at the integration target sites of many retroviruses
  2. Wu, X. L.; Li, Y.; Crise, B.; Burgess, S. M.; Munroe, D. J.
  3. Journal of Virology. 2005, APR; 79(8): 5211-5214.
  1. 20.   Genetic recombination of human immunodeficiency virus type 1 in one round of viral replication: Effects of genetic distance, target cells, accessory genes, and lack of high negative interference in crossover events
  2. Rhodes, T. D.; Nikolaitchik, O.; Chen, J. B.; Powell, D.; Hu, W. S.
  3. Journal of Virology. 2005, FEB; 79(3): 1666-1677.
  1. 21.   Cytotoxicity of RH1: NAD(P)H : quinone acceptor oxidoreductase (NQO1)-independent oxidative stress and apoptosis induction
  2. Tudor, G.; Alley, M.; Nelson, C. M.; Huang, R. L.; Covell, D. G.; Gutierrez, P.; Sausville, E. A.
  3. Anti-Cancer Drugs. 2005 16(4): 381-391.
  1. 22.   Linking pathway gene expressions to the growth inhibition response from the National Cancer Institute's anticancer screen and drug mechanism of action
  2. Huang, R.; Wallqvist, A.; Thanki, N.; Covell, D. G.
  3. Pharmacogenomics Journal. 2005 5(6): 381-399.
  1. 23.   Comparison of the genomic structure and variation in the two human sodium-dependent vitamin C transporters, SLC23A1 and SLC23A2
  2. Eck, P.; Erichsen, H. C.; Taylor, J. G.; Yeager, M.; Hughes, A. L.; Levine, M.; Chanock, S. J.
  3. Human Genetics. 2004, SEP; 115(4): 285-294.
  1. 24.   Expressions of hepatic genes, especially IGF-binding protein-1, correlating with serum corticosterone in microarray analysis
  2. Cheng, R. Y. S.; Birely, L. A.; Lum, N. L.; Perella, C. M.; Cherry, J. M.; Bhat, N. K.; Kasprzak, K. S.; Powell, D. A.; Alvord, W. G.; Anderson, L. M.
  3. Journal of Molecular Endocrinology. 2004 32(1): 257-278.
  1. 25.   Association of strong virus-specific CD4 T cell responses with efficient natural control of primary HIV-1 infection
  2. Gloster, S. E.; Newton, P.; Cornforth, D.; Lifson, J. D.; Williams, I.; Shaw, G. M.; Borrow, P.
  3. Aids. 2004 18(5): 749-755.
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