Full Text Journal Articles by
Author Anastasia K Yocum

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The central role of EED in the orchestration of polycomb group complexes.

Qi Cao, Xiaoju Wang, Meng Zhao, Rendong Yang, Rohit Malik, Yuanyuan Qiao, Anton Poliakov, Anastasia K Yocum, Yong Li, Wei Chen, Xuhong Cao, Xia Jiang, Arun Dahiya, Clair Harris, Felix Y Feng, Sundeep Kalantry, Zhaohui S Qin, Saravana M Dhanasekaran, Arul M Chinnaiyan,

Polycomb repressive complexes 1 and 2 (PRC1 and 2) play a critical role in the epigenetic regulation of transcription during cellular differentiation, stem cell pluripotency and neoplastic progression. Here we show that the polycomb group protein EED, a core component of PRC2, physically interacts with and functions as part of ... Read more >>

Nat Commun (Nature communications)
[2014, 5:3127]

Cited: 48 times

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Characterization of KRAS rearrangements in metastatic prostate cancer.

Xiao-Song Wang, Sunita Shankar, Saravana M Dhanasekaran, Bushra Ateeq, Atsuo T Sasaki, Xiaojun Jing, Daniel Robinson, Qi Cao, John R Prensner, Anastasia K Yocum, Rui Wang, Daniel F Fries, Bo Han, Irfan A Asangani, Xuhong Cao, Yong Li, Gilbert S Omenn, Dorothee Pflueger, Anuradha Gopalan, Victor E Reuter, Emily Rose Kahoud, Lewis C Cantley, Mark A Rubin, Nallasivam Palanisamy, Sooryanarayana Varambally, Arul M Chinnaiyan,

Using an integrative genomics approach called amplification breakpoint ranking and assembly analysis, we nominated KRAS as a gene fusion with the ubiquitin-conjugating enzyme UBE2L3 in the DU145 cell line, originally derived from prostate cancer metastasis to the brain. Interestingly, analysis of tissues revealed that 2 of 62 metastatic prostate cancers ... Read more >>

Cancer Discov (Cancer discovery)
[2011, 1(1):35-43]

Cited: 54 times

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Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis.

Damian Fermin, Venkatesha Basrur, Anastasia K Yocum, Alexey I Nesvizhskii,

We describe Abacus, a computational tool for extracting spectral counts from MS/MS data sets. The program aggregates data from multiple experiments, adjusts spectral counts to accurately account for peptides shared across multiple proteins, and performs common normalization steps. It can also output the spectral count data at the gene level, ... Read more >>

Proteomics (Proteomics)
[2011, 11(7):1340-1345]

Cited: 43 times

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Development of selected reaction monitoring-MS methodology to measure peptide biomarkers in prostate cancer.

Anastasia K Yocum, Amjad P Khan, Rong Zhao, Arul M Chinnaiyan,

Prostate cancer is a leading cause of cancer-related death. The current modality of diagnosis, the measurement of serum PSA, not only suffers from lack of specificity, but does not distinguish clinical cases in which current treatment measures would be most successful, i.e. aggressive, life-threatening tumors. A multiplexed MS methodology, selected ... Read more >>

Proteomics (Proteomics)
[2010, 10(19):3506-3514]

Cited: 18 times

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A spectral clustering approach to MS/MS identification of post-translational modifications.

Jayson A Falkner, Jarret W Falkner, Anastasia K Yocum, Philip C Andrews,

Unidentified tandem mass spectra typically represent 50-90% of the spectra acquired in proteomics studies. This manuscript describes a novel algorithm, "Bonanza", for clustering spectra without knowledge of peptide or protein identifications. Further analysis leverages existing peptide identifications to infer related, likely valid identifications. Significantly more spectra can be identified with ... Read more >>

J. Proteome Res. (Journal of proteome research)
[2008, 7(11):4614-4622]

Cited: 27 times

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EBP, a program for protein identification using multiple tandem mass spectrometry datasets.

Thomas S Price, Margaret B Lucitt, Weichen Wu, David J Austin, Angel Pizarro, Anastasia K Yocum, Ian A Blair, Garret A FitzGerald, Tilo Grosser,

MS/MS combined with database search methods can identify the proteins present in complex mixtures. High throughput methods that infer probable peptide sequences from enzymatically digested protein samples create a challenge in how best to aggregate the evidence for candidate proteins. Typically the results of multiple technical and/or biological replicate experiments ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2007, 6(3):527-536]

Cited: 33 times

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Proteomics-based strategy to identify biomarkers and pharmacological targets in leukemias with t(4;11) translocations.

Anastasia K Yocum, Christine M Busch, Carolyn A Felix, Ian A Blair,

Translocations and other aberrations involving the MLL (mixed lineage leukemia) gene result in aggressive forms of leukemias. Heterogeneity in partner genes, in chromosomal breakpoints, in MLL itself, and in the different partner genes results in heterogeneous fusion transcripts that can be alternatively spliced, which complicates deciphering a unifying mechanism of ... Read more >>

J. Proteome Res. (Journal of proteome research)
[2006, 5(10):2743-2753]

Cited: 21 times

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Novel lipid hydroperoxide-derived hemoglobin histidine adducts as biomarkers of oxidative stress.

Anastasia K Yocum, Tomoyuki Oe, Alfred L Yergey, Ian A Blair,

Hemoglobin (Hb) adducts have long been used as dosimeters of exposure to xenobiotics and endogenously formed reactive metabolites. In this study, hemoglobin chains were separated from each other and their prosthetic heme groups and reacted with 4-oxo-2-nonenal, a major breakdown product of lipid hydroperoxides. The adducts were characterized by matrix-assisted ... Read more >>

J Mass Spectrom (Journal of mass spectrometry : JMS)
[2005, 40(6):754-764]

Cited: 16 times

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Effect of immunoaffinity depletion of human serum during proteomic investigations.

Anastasia K Yocum, Kenneth Yu, Tomoyuki Oe, Ian A Blair,

Controversy exists regarding the proper mining of the human serum proteome. Because of the analytical challenges of accurately measuring samples containing a very large dynamic range of protein concentrations, current practices have employed depletion of the highly abundant housekeeping serum proteins, such as albumin and immunoglobins. There is question as ... Read more >>

J. Proteome Res. (Journal of proteome research)
[2005, 4(5):1722-1731]

Cited: 61 times

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