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SCIENTIFIC REPORTS, ISSN 2045-2322, 05/2019, Volume 9, Issue 1, pp. 6980 - 10
The National Cancer Institute conducted the Biospecimen Pre-analytical Variables (BPV) study to determine the effects of formalin fixation and delay to... 
QUALITY | PROTEIN | MULTIDISCIPLINARY SCIENCES | TISSUE | GENE-EXPRESSION | VALIDATION | ISCHEMIA TIME | Next-generation sequencing | Gene expression | Formaldehyde | Freezing | MiRNA
Journal Article
Oncotarget, ISSN 1949-2553, 2014, Volume 5, Issue 13, pp. 4788 - 4798
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 2/2012, Volume 109, Issue 8, pp. 3053 - 3058
Journal Article
PLoS ONE, ISSN 1932-6203, 06/2015, Volume 10, Issue 6, p. e0128557
Background Inflammation and immune activation of the cervicovaginal mucosa are considered factors that increase susceptibility to HIV infection. Therefore, it... 
TOPICAL MICROBICIDES | CCR6-EXPRESSING TH17 CELLS | CERVICOVAGINAL INFLAMMATION | EPITHELIAL-CELLS | IMMUNE-RESPONSES | MULTIDISCIPLINARY SCIENCES | TOLL-LIKE RECEPTORS | NEISSERIA-GONORRHOEAE | SEXUAL TRANSMISSION | T-CELLS | BACTERIAL VAGINOSIS | Inflammation - pathology | Transcription, Genetic - drug effects | Oligonucleotide Array Sequence Analysis | Anti-Infective Agents - pharmacology | Humans | Bacteria - drug effects | NF-kappa B - metabolism | Gene Expression Profiling | Colony Count, Microbial | Gene Regulatory Networks - drug effects | Microbial Sensitivity Tests | Bacteria - growth & development | Female | Mucous Membrane - drug effects | Drug Evaluation, Preclinical | Real-Time Polymerase Chain Reaction | Vagina - cytology | Biomarkers - metabolism | Cell Line | Reproducibility of Results | Anti-Infective Agents - therapeutic use | Mucous Membrane - pathology | Models, Biological | HIV Infections - drug therapy | Vagina - microbiology | Immunologic Factors - pharmacology | Cluster Analysis | Microbiota (Symbiotic organisms) | Genes | Comparative analysis | Gene expression | HIV (Viruses) | Health aspects | HIV infection | Risk factors | Deregulation | Profiling | Laboratories | Mucosa | Cellulose | Clinical trials | Biology | Infections | Activation | Medical schools | Vaginosis | Microbiota | Microbicides | Lymphocytes | Human immunodeficiency virus--HIV | Bacteria | Bioindicators | Bioinformatics | Medical research | NF-κB protein | Evaluation | Immune response | Young adults | Immunomodulation | Gynecology | Vagina | Data processing | Inflammation | Functional analysis | Obstetrics | Disease transmission | DNA microarrays | Biomarkers | In vitro methods and tests | Cancer | HIV | Human immunodeficiency virus
Journal Article
Clinical Chemistry, ISSN 0009-9147, 12/2012, Volume 58, Issue 12, pp. 1720 - 1722
Journal Article
Oncogene, ISSN 0950-9232, 06/2011, Volume 30, Issue 23, pp. 2633 - 2643
Misregulation of the canonical Wnt/beta-catenin pathway and aberrant activation of Wnt signaling target genes are common in colorectal cancer (CRC) and... 
HEF1 | Wnt signaling | colorectal cancer | tumorigenesis | PATHWAYS | ACTIVATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | BETA-CATENIN | CELL BIOLOGY | ONCOLOGY | COLORECTAL-CANCER | GENETICS & HEREDITY | MUTATIONS | TRANSCRIPTIONAL REGULATION | EXPRESSION | CARCINOMA | PROSTAGLANDIN E-2 | ENDOTHELIAL GROWTH-FACTOR | Colon - cytology | Colorectal Neoplasms - genetics | Humans | Gene Expression Regulation, Neoplastic | Transplantation, Heterologous | Phosphoproteins - metabolism | Wnt Proteins - metabolism | Promoter Regions, Genetic - genetics | Neoplasms, Experimental - pathology | TCF Transcription Factors - metabolism | RNA Interference | Mice, Mutant Strains | Neoplasms, Experimental - genetics | Colorectal Neoplasms - metabolism | Caco-2 Cells | Cell Line | Signal Transduction | Mice, Inbred C57BL | Phosphoproteins - genetics | Reverse Transcriptase Polymerase Chain Reaction | beta Catenin - metabolism | Blotting, Western | Colon - metabolism | Disease Progression | beta Catenin - genetics | HT29 Cells | Animals | Mice, Nude | Adaptor Proteins, Signal Transducing - genetics | Cell Line, Tumor | Protein Binding | Mice | Neoplasms, Experimental - metabolism | Adaptor Proteins, Signal Transducing - metabolism | Colorectal Neoplasms - pathology | Cell Movement | Colorectal cancer | Development and progression | Genetic aspects | Cellular signal transduction | Research | Carcinogenesis | Risk factors | Proteins | Signal transduction | Gene expression | Cell adhesion & migration
Journal Article
Journal Article
Journal of Ethnopharmacology, ISSN 0378-8741, 2010, Volume 127, Issue 1, pp. 98 - 102
Journal Article
Genomics, ISSN 0888-7543, 12/2014, Volume 104, Issue 6, pp. 453 - 458
Several studies have demonstrated that unmapped reads in next generation sequencing data could be used to identify infectious agents or structural variants,... 
Non-human sequences | Unmapped reads | Sequencing contamination | EXOME CAPTURE | HUMAN GENOMES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | DNA, Viral - chemistry | DNA, Bacterial - chemistry | DNA, Plant - chemistry | Genome, Human | DNA Contamination | Humans | Comparative analysis | Genomics | Genomes | Index Medicus | non-human sequences
Journal Article
Bioinformatics, ISSN 1367-4803, 07/2013, Volume 29, Issue 14, pp. 1734 - 1741
Journal Article
BioData Mining, ISSN 1756-0381, 11/2014, Volume 7, Issue 1, pp. 25 - 25
Background: Many bacterial genome sequences completed using the Sanger method may contain assembly errors due in-part to low sequence coverage driven by cost.... 
Mycobacterium | Salmonella | Microbiota | Sequences | Genomics | Brucella | Bacteria | Genomes | Vibrio | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Microbiota (Symbiotic organisms) | Series (mathematics) | Genetics | Assembly | Gene sequencing
Journal Article
by Vasaikar, Suhas and Huang, Chen and Wang, Yi-Ting and Wang, Xiaojing and Wang, Yue and Petyuk, Vladislav A and Savage, Sara R and Wen, Bo and Dou, Yongchao and Zhang, Zhen and Zhang, Hui and Zhang, Bing and Zhang, Yun and Shi, Zhiao and Arshad, Osama A and Gritsenko, Marina A and Zimmerman, Lisa J and McDermott, Jason E and Clauss, Therese R and Moore, Ronald J and Zhao, Rui and Zhao, Yingming and Monroe, Matthew E and Chambers, Matthew C and Slebos, Robert J.C and Slebos, Robbert J.C and Lau, Ken S and Mo, Qianxing and Ding, Li and Ellis, Matthew and Ellis, Matthew J.C and Thiagarajan, Mathangi and Kinsinger, Christopher R and Rodriguez, Henry and Smith, Richard D and Rodland, Karin D and Liebler, Daniel C and Liu, Tao and Bavarva, Jasmin and Borucki, Melissa and Elburn, Kimberly and Hannick, Linda and Vatanian, Negin and Payne, Samuel H and Carr, Steven A and Clauser, Karl R and Gillette, Michael A and Kuhn, Eric and Mani, D.R and Cai, Shuang and Ketchum, Karen A and Thangudu, Ratna R and Whiteley, Gordon A and Paulovich, Amanda and Whiteaker, Jeff and Edward, Nathan J and Madhavan, Subha and McGarvey, Peter B and Chan, Daniel W and Shih, Ie-Ming and Zhu, Heng and Skates, Steven J and White, Forest M and Mertins, Philip and Pandey, Akhilesh and Boja, Emily and Hiltke, Tara and Mesri, Mehdi and Rivers, Robert C and Stein, Stephen E and Fenyo, David and Ruggles, Kelly and Levine, Douglas A and Oberti, Mauricio and Rudnick, Paul A and Snyder, Michael and Tabb, David L and Chen, Xian and Ransohoff, David F and Hoofnagle, Andrew and Sanders, Melinda E and Davies, Sherri R and Townsend, R. Reid and Watson, Mark and Clinical Proteomic Tumor Analysis and Clinical Proteomic Tumor Analysis Consortium
Cell, ISSN 0092-8674, 05/2019, Volume 177, Issue 4, pp. 1035 - 1049.e19
We performed the first proteogenomic study on a prospectively collected colon cancer cohort. Comparative proteomic and phosphoproteomic analysis of paired... 
RB1 | tumor antigen | proteomics | immune evasion | colon cancer | biomarkers | glycolysis | drug targets | SOX9 | proteogenomics | TANDEM MASS-SPECTRA | READ ALIGNMENT | DATABASE | HIGH-THROUGHPUT | COLORECTAL-CANCER | BIOCHEMISTRY & MOLECULAR BIOLOGY | IDENTIFICATION | TUMORS | SOFTWARE | SEQ | TOOL | CELL BIOLOGY | Proteins | Prevention | Antigens | Glucose metabolism | Medical colleges | Colon cancer | Analysis | Gastrointestinal diseases | T cells | Health aspects | Tumors | Cancer
Journal Article
Oncotarget, ISSN 1949-2553, 2014, Volume 5, Issue 15, pp. 6003 - 6014
Journal Article
Aging, ISSN 1945-4589, 06/2014, Volume 6, Issue 6, pp. 511 - 521
A singular genome used for inference into population-based studies is a standard method in genomics. Recent studies show that spontaneous genomic variants can... 
AUTISM | GENETIC-VARIANTS | CANCER | GENOME | DAMAGE | personalized medicine | CELL BIOLOGY | GERIATRICS & GERONTOLOGY | exome sequencing | EVOLUTION | DE-NOVO MUTATIONS | DATABASE | Aging | dynamic exome | personalized genomics | DNA-SEQUENCING DATA | EXPRESSION
Journal Article